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Affymetrix GeneChip

Genotyping

Analysis Software Version 4.1 —

User's Guide

P/N 702083 Rev. 2

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Page 1 Affymetrix GeneChip ® Genotyping Analysis Software Version 4.1 — User’s Guide P/N 702083 Rev. 2...
Page 2 For research use only. Not for use in diagnostic procedures. Trademarks ® ® ® ® ® ™ Affymetrix , GeneChip , HuSNP , GenFlex , Flying Objective ® ® ™ ® CustomExpress , CustomSeq , NetAffx , Tools To Take You As Far As Your Vision ™...
Page 3: Table Of Contents
Table of Contents Introduction ABOUT THIS MANUAL CONVENTIONS USED IN THIS GUIDE ONLINE DOCUMENTATION TECHNICAL SUPPORT CHAPTER 1 GTYPE Overview GTYPE ANALYSIS USING GTYPE WITH GCOS GTYPE WALKTHROUGH MAPPING ANALYSIS WORKFLOW UNIVERSAL TAG WORKFLOW CHAPTER 2 Getting Started OPTIONS FOR USING GTYPE STARTING GTYPE USER INTERFACE COMPONENTS DATA TREE...
Page 4 Affymetrix GeneChip ® Genotyping Analysis Software User’s Guide CHAPTER 3 Working with Images VIEWING CELL INTENSITY IMAGES ADJUSTING THE IMAGE SETTINGS VIEWING PROBE CELL DATA VIEWING PROBE SET INTENSITY DATA BOOKMARKS DEFAULT IMAGE SETTINGS CHAPTER 4 Analyzing Cell Intensity Data OVERVIEW USING THE ANALYZE DIALOG BOX USING THE DATA TREE...
Page 5 Contents MAPPING ANALYSIS – GENOTYPE CALLS SNP TABLE SCATTER PLOTS CHAPTER 6 Working with Mapping Data SETTING UP SAMPLE ATTRIBUTES IMPORTING PEDIGREE/ATTRIBUTE INFORMATION DISPLAYING DATA IN VIRTUAL ARRAYS CHECKING FOR MENDELIAN INHERITANCE ERROR USING THE SAMPLE MISMATCH REPORT TOOL EXPORTING DATA WITH THE SNP EXPORT TOOL LOSS OF HETEROZYGOSITY ANALYSIS CHAPTER 7 Universal Tag Window...
Page 6 Affymetrix GeneChip ® Genotyping Analysis Software User’s Guide ™ CHAPTER 9 NetAffx Annotations OVERVIEW ™ DOWNLOADING NETAFFX ANNOTATIONS SELECTING ANNOTATIONS FOR DISPLAY SETTING THE ADVANCED OPTIONS CHAPTER 10 Reports OVERVIEW WORKING WITH REPORTS Appendix A Installing GTYPE Software OVERVIEW REQUIREMENTS INSTALLATION SELECTING A DATABASE INSTALLING GTYPE SERVER COMPONENTS...
Page 7 Contents MPAM MAPPING ALGORITHM SETTINGS Appendix C Dynamic Model Mapping Algorithm THE DYNAMIC MODEL MAPPING ARRAY THE DYNAMIC MODEL MAPPING ALGORITHM DYNAMIC MODEL MAPPING ALGORITHM SETTINGS Appendix D Bayesian Robust Linear Model with Mahalanobis (BRLMM) Distance Classifier Algorithm INTRODUCTION NORMALIZATION AND ALLELE SUMMARIZATION CLUSTERING SPACE TRANSFORMATION CALLING GENOTYPES ESTIMATING CLUSTER CENTERS AND VARIANCES...
Page 8 viii Affymetrix GeneChip ® Genotyping Analysis Software User’s Guide Appendix E Mapping Tool Algorithms SAMPLE MISMATCH ALGORITHM FILTER ALGORITHMS Appendix F IUPAC Base Codes Appendix G File Types Appendix H Working with Windowpanes & Columns Appendix I Hot Key Descriptions Index...
Page 9 Introduction...
Page 11: Introduction
Introduction Welcome to the Affymetrix GeneChip ® Genotyping Analysis Software (GTYPE) User’s Guide. The GTYPE 4.1 software ® (PN 690051) is part of the GeneChip mapping array system, specifically designed to give highly accurate, automated, SNP allele ® calls for the GeneChip mapping arrays.
Page 12: About This Manual
Affymetrix GeneChip ® Genotyping Analysis Software User’s Guide • A Virtual Array feature, which allows the 100K Array Set and/or 500K Array Set to be managed as a single-array data set • The FileSets feature, which allows customized groupings of samples from multiple projects About this Manual This manual presents information about the GTYPE software in the...
Page 13 Welcome The appendices include additional information and reference information: • Appendix A, Installing GTYPE Software: Provides installation instructions and information on initializing GTYPE. • Appendix B, MPAM Mapping Algorithm: Describes the Modified Partitioning Around Medoids (MPAM) mapping algorithm and the user-definable parameters. •...
Page 14: Conventions Used In This Guide
Affymetrix GeneChip ® Genotyping Analysis Software User’s Guide Conventions Used in This Guide This manual provides a detailed outline for all tasks associated with Affymetrix ® GTYPE software. Various conventions are used throughout the manual to help illustrate the procedures described. Explanations of these conventions are provided below.
Page 15 Welcome SCREEN CAPTURES The steps outlining procedures are frequently supplemented with screen captures to further illustrate the instructions given. The screen captures depicted in this manual may not exactly match the windows displayed on your screen. ADDITIONAL COMMENTS Throughout the manual, text and procedures are occasionally accompanied by special notes.
Page 16: Online Documentation
Affymetrix GeneChip ® Genotyping Analysis Software User’s Guide Warnings alert you to situations where physical harm to person or damage to hardware is possible. Online Documentation The CD with the GTYPE software includes an electronic version of this guide. The electronic version is in Adobe Acrobat format (a *.pdf file) and is readable with the Adobe Acrobat Reader software, available at no charge from Adobe at http://www.adobe.com.
Page 17: Technical Support
Welcome Technical Support Affymetrix provides technical support to all licensed users via phone or E-mail. To contact Affymetrix ® Technical Support: AFFYMETRIX, INC. 3420 Central Expressway Santa Clara, CA 95051 USA Tel: 1-888-362-2447 (1-888-DNA-CHIP) Fax: 1-408-731-5441 sales@affymetrix.com support@affymetrix.com AFFYMETRIX UK Ltd., Voyager, Mercury Park, Wycombe Lane, Wooburn Green, High Wycombe HP10 0HH...
Page 18 Affymetrix GeneChip ® Genotyping Analysis Software User’s Guide...
Page 19 GTYPE Overview Chapter...
Page 20 Chapter...
Page 21: Gtype Overview
GTYPE Overview GTYPE (Affymetrix GeneChip ® Genotyping Analysis Software, PN 690051) is part of an integrated suite of software applications that allows you to: ® • Perform analysis of different GeneChip probe array experiments • Analyze the data from those experiments •...
Page 22 Affymetrix GeneChip ® Genotyping Analysis Software User’s Guide • Import attributes such as pedigree data for the sample (see Importing Pedigree/Attribute Information, on page 185). • Use the SNP data and imported pedigree data for Mendelian error checking (see Checking for Mendelian Inheritance Error, on page 201).
Page 23 Chapter 1 | GTYPE Overview 100K AND 500K MAPPING ARRAYS ® The Affymetrix GeneChip Human Mapping 100K and 500K array sets provide an efficient method for genotyping more than 100,000 SNPs using a two-array set. Each SNP that can be detected with the array has a group of probes, known as a probe set.
Page 24: Using Gtype With Gcos
Affymetrix GeneChip ® Genotyping Analysis Software User’s Guide For more information about the algorithm and the model, see Appendix D, Bayesian Robust Linear Model with Mahalanobis (BRLMM) Distance Classifier Algorithm, on page 353. GENFLEX ® TAG ARRAY ® The GenFlex Tag Array uses nucleic acid hybridization to parse as many as 2000 individual reaction products from complex pooled mixtures.
Page 25 Chapter 1 | GTYPE Overview GTYPE In GTYPE, you can: • View the cell intensity data as an image (see Chapter 3, Working with Images, on page • Analyze the cell intensity data for: ® - GeneChip 10K, 100K, and 500K mapping arrays ®...
Page 26 Affymetrix GeneChip ® Genotyping Analysis Software User’s Guide - DM mapping analysis data (see Exporting Data from the SNP Table, on page 159) - MPAM and DM mapping analysis data and pedigree information for association and linkage analysis (see Exporting Data with the SNP Export Tool, on page 226) - Universal Tag Analysis data (see...
Page 27: Gtype Walkthrough
Chapter 1 | GTYPE Overview GTYPE Walkthrough USER INTERFACE COMPONENTS Menu bar Toolbar Data tree Main display area Shortcut Status Figure 1.1 GTYPE user interface at startup The GTYPE user interface (Figure 1.1) includes the following windowpanes: • Data tree: Provides easy access to the experiment information, cell intensity data, and analysis results •...
Page 28 Affymetrix GeneChip ® Genotyping Analysis Software User’s Guide • Main Display Area: Displays the analysis results, the Batch Analysis window, and the reports • Status Log: displays system status messages Selecting Different Data in the Data Tree Classic View Project View Project Name Sample Name Experiment Information...
Page 29 Chapter 1 | GTYPE Overview Data Tree Functions for Project and Sample Information Right-click the Project or Sample file to view the shortcut menu Rename a sample or project Figure 1.3 Data tree functions for Project and Sample information...
Page 30 Affymetrix GeneChip ® Genotyping Analysis Software User’s Guide Data Tree Functions for Experiment Information Open an experiment file Right-click the Experiment information file to view the shortcut menu View information about the experiment Rename the experiment Figure 1.4 Data tree functions for experiment information (GTYPE)
Page 31 Chapter 1 | GTYPE Overview Data Tree Functions for Mapping Analysis Results Display analysis results in: MPAM Mapping Analysis window Right-click the selected analysis results files to view the shortcut menu Dynamic Model Mapping Analysis window Create a Mapping Analysis report (*.rpt) for the selected analysis results files View information about the analysis results file...
Page 32 Affymetrix GeneChip ® Genotyping Analysis Software User’s Guide Data Tree Functions for Universal Tag Analysis Results Display analysis results in the Universal Tag window Right-click the selected analysis results files to view the shortcut menu View information about the analysis results file Figure 1.6 Data tree functions for Universal Tag analysis results...
Page 33 Chapter 1 | GTYPE Overview Data Tree Functions for FileSets Open the FileSets dialog box to create a new FileSet Right-click the FileSets header to view the shortcut menu Open the FileSets dialog box to add or delete files from the selected FileSet Right-click a FileSet to view the shortcut menu Rename the selected FileSet...
Page 34 Affymetrix GeneChip ® Genotyping Analysis Software User’s Guide Tools Shortcut Bar For detailed information see Shortcut Bar - Tools, on page Click a button to change the view in the main display area Figure 1.8 GTYPE Shortcut bar, Tools...
Page 35 Chapter 1 | GTYPE Overview Settings Shortcut Bar Functions Change defaults for image settings, servers, and analys Click a button to: Select categories of data for display in the data tree Change the MPAM and Dynamic Model Mapping algorithm settings Figure 1.9 GTYPE Shortcut bar, Settings...
Page 36: Mapping Analysis Workflow
Affymetrix GeneChip ® Genotyping Analysis Software User’s Guide Mapping Analysis Workflow Mapping Analysis works with Mapping arrays, such as the Affymetrix GeneChip Mapping 10K Array, and Affymetrix ® ® ® GeneChip Human Mapping 100K and 500K Sets. ® The GTYPE Mapping Analysis workflow allows you to: •...
Page 37 Chapter 1 | GTYPE Overview To import and use attributes you must first: • Set up a sample template with attributes for pedigree data in GCOS Manager. • Use this template when registering the mapping samples and experiments in GCOS. •...
Page 38 Affymetrix GeneChip ® Genotyping Analysis Software User’s Guide ANALYZING CELL INTENSITY DATA toolbar 1. To open the Batch Analysis window, click the Batch Analysis shortcut bar button. Drag the cell intensity data for analysis to the Batch Analysis Window. 2. To run the analysis, click the Run Analysis toolbar button.
Page 39 Chapter 1 | GTYPE Overview CREATING A VIRTUAL SET A virtual set combines data from two different array designs run with the same sample. Grouping the data into these sets simplifies downstream analysis and manipulation. Before using the VirtualSet Tool, you must assign sample attribute data that will identify arrays run with the same sample.
Page 40 Affymetrix GeneChip ® Genotyping Analysis Software User’s Guide B. To create a VirtualSet group: 1. Select analysis data from different arrays and samples in the Data Tree. 2. Right-click on the selected data and select Open from the short-cut menu. The VirtualSet Creation dialog box opens.
Page 41 Chapter 1 | GTYPE Overview DISPLAYING MAPPING ANALYSIS DATA Mapping analysis data is displayed in: • Dynamic Model Mapping Analysis window (Figure 1.14). • MPAM Mapping Analysis window (Figure 1.15). • BRLMM Analysis Window (displays SNP table only) The Dynamic Model Mapping Analysis window displays the results in the DM Scatter Plot and the DM SNP table. For more information, see Chapter 5, Mapping Analysis Window, on page 137.
Page 42 Affymetrix GeneChip ® Genotyping Analysis Software User’s Guide The MPAM Mapping Analysis window displays the results in the RAS scatter plot and the MPAM SNP table. For more information, see Chapter 5, Mapping Analysis Window, on page 137. Figure 1.15 Viewing MPAM Mapping Analysis results...
Page 43 Chapter 1 | GTYPE Overview VIEWING INTENSITY DATA IN THE PROBE INTENSITY WINDOW Click the Probe Intensity button to For more information see Chapter 8, Probe Intensity Window, evaluate probe cell intensities for a on page 261. selected SNP in the Probe Intensity Window.
Page 44 Affymetrix GeneChip ® Genotyping Analysis Software User’s Guide PERFORMING A PEDIGREE CHECK Before performing a pedigree check, you must import pedigree data. Pedigree Check allows you to test for errors in Mendelian inheritance. To perform a pedigree check: → 1. Select Tools Pedigree Check...
Page 45 Chapter 1 | GTYPE Overview SNPs that do not meet Mendelian inheritance rules are displayed in a text file that can be viewed in spreadsheet software For more information, see Checking for Mendelian Inheritance Error, on page 201. Figure 1.18 Viewing Pedigree Check results...
Page 46 Affymetrix GeneChip ® Genotyping Analysis Software User’s Guide PERFORMING A SAMPLE MATCH TEST The Sample Match report allows you to identify .chp files with the same SNP calls for a group of SNPs. To perform a Sample Match check: → 1.
Page 47 Chapter 1 | GTYPE Overview .CHP file pairs with discrepancies of some sort are displayed in a report that can be viewed in Notepad or spreadsheet software. The Sample Match report displays a list of .CHP file pairs with the same SNP pattern (different samples from the same person).
Page 48 Affymetrix GeneChip ® Genotyping Analysis Software User’s Guide PERFORMING A SAMPLE MISMATCH TEST The Sample Mismatch report allows you to find .chp files that have been mislabeled or have other problems. Before performing a sample mismatch check, you must import pedigree data.
Page 49 Chapter 1 | GTYPE Overview .CHP file pairs with discrepancies of some sort are displayed in a report that can be viewed in Notepad or spreadsheet software. Depending upon the attribute information you provide, the Sample Mismatch report displays: • A list of .CHP file pairs with discrepancies between the sample and person giving the sample. •...
Page 50 Affymetrix GeneChip ® Genotyping Analysis Software User’s Guide Exporting SNP Data in Tab-Delimited Format To export SNP data in Tab-delimited format: → 1. Select Tools SNP Export from the menu bar; or Click the Export button in the Shortcut bar. The SNP Export dialog box opens.
Page 51 Chapter 1 | GTYPE Overview Exporting SNP Data for Association and Linkage Analysis Software Before exporting SNP data for linkage analysis, you must import pedigree data. To perform an association or linkage export: → 1. Select Tools SNP Export from the menu bar; or Click the Export button in the Shortcut bar.
Page 52: Universal Tag Workflow
Affymetrix GeneChip ® Genotyping Analysis Software User’s Guide Universal Tag Workflow The Universal Tag workflow allows you to: • Analyze the tag intensity data (Figure 1.25) • Display and export the analysis results (Figure 1.26) 1. Right-click on selected cell intensity data files in the data tree.
Page 53 Chapter 1 | GTYPE Overview 4. In the data tree, double-click the analysis results that you want to view. 5. In the Tag table, copy and paste selected rows to the system clipboard for export to tabular format. For more information, see Chapter 7, Universal Tag Window, on page 253.
Page 54 Affymetrix GeneChip ® Genotyping Analysis Software User’s Guide...
Page 55 Getting Started Chapter...
Page 56 Chapter...
Page 57: Getting Started
Getting Started This chapter contains the following sections: • Options for Using GTYPE (see below) • Starting GTYPE (see page 50) • User Interface Components (see page 54) Options for Using GTYPE ® GTYPE analyzes cell intensity data for Affymetrix GeneChip ®...
Page 58: Starting Gtype
Affymetrix GeneChip ® Genotyping Analysis Software User’s Guide ® • Affymetrix GeneChip Library Install • GCOS Manager USING GTYPE WITH GCOS SERVER You can use GTYPE with a remote GCOS Server database on a network if the database administrator has loaded the necessary library and data files.
Page 59 Chapter 2 | Getting Started Click the Windows Start menu button and select Programs Affymetrix GTYPE. At start up, the main window displays the data tree, shortcut bar, and status log (Figure 2.1). Menu bar Toolbar Data tree Main display area Shortcut bar Status log Figure 2.1...
Page 60 Affymetrix GeneChip ® Genotyping Analysis Software User’s Guide The Defaults dialog box opens. Figure 2.2 Defaults dialog box, Database Options tab Click the Database tab to display the Database Options (Figure 2.2). You can learn more about the other Defaults tabs in: Making Global Adjustments to Subsequently Opened Images, on page 85 Analysis Defaults, on page 135...
Page 61 Chapter 2 | Getting Started Select Tools Filters from the menu bar. The Filters dialog box opens (Figure 2.3). Figure 2.3 GTYPE Filters dialog box Select the Assay type from the Assay Type drop-down box. Click OK to close the Filters dialog box. The data tree displays the data for the selected assay type.
Page 62: User Interface Components
Affymetrix GeneChip ® Genotyping Analysis Software User’s Guide User Interface Components Menu bar Toolbar Data tree Main display area Shortcut bar Status log Figure 2.4 GTYPE user interface at start up The GTYPE user interface provides the following components: • Data tree: Displays data available in GTYPE for the selected Assay type (see Data Tree, on page 57).
Page 63 Chapter 2 | Getting Started • Main display area: Displays the following types of information: - Cell intensity data (see Chapter 3, Working with Images, on page - Files selected for analysis (see Using the Batch Analysis Window, on page 117) - MPAM, DM, and BRLMM mapping analysis results (see Chapter 5, Mapping Analysis Window, on page...
Page 64 Affymetrix GeneChip ® Genotyping Analysis Software User’s Guide Main Toolbar Figure 2.5 Main toolbar You can display toolbars with text labels (Figure 2.5). To display the toolbar button labels, select View Toolbar Text Labels from the menu bar. Table 2.1 Main toolbar button functions Menu Bar Command Toolbar...
Page 65: Data Tree
Chapter 2 | Getting Started Table 2.1 Main toolbar button functions Menu Bar Command Toolbar Function Button Batch Analysis, or Performs analysis on displayed cell intensity data in the Image window. Disabled unless cell intensity data is displayed in the BRLMM Batch Image window.
Page 66 Affymetrix GeneChip ® Genotyping Analysis Software User’s Guide Classic View Project View Project Name Sample Name Experiment Information Cell Intensity Data Analysis Results FileSets Right-click anywhere in the data tree and select the view Figure 2.6 GTYPE Data tree In the data tree, you can perform the following tasks: •...
Page 67 Chapter 2 | Getting Started • Rename Projects, Samples, and Experiments (see page 69). To hide or display the data tree: - Click the data tree button in the Main toolbar. OVERVIEW The data tree provides two ways to display the data: •...
Page 68 Affymetrix GeneChip ® Genotyping Analysis Software User’s Guide • Cell Intensity data files (with .cel extension) • Analysis Results data files (with .chp extension) • FileSets (groups of files with .gfs extension) The Project, Sample, and Experiment categories are assigned during the creation of experiments and the importation of data in GCOS.
Page 69 Chapter 2 | Getting Started The data tree displays the files for the selected assay type and categories. The Filters applied notice appears in the lower right corner of the GTYPE window. You can also use the Filter categories to screen files when using the File menu commands to open and analyze data.
Page 70 Affymetrix GeneChip ® Genotyping Analysis Software User’s Guide VIEWING FILE INFORMATION To view file information: • In the data tree, right-click an item (experiment information, cell intensity data, or analysis results) and select Information from the shortcut menu. Information about the selected item(s) is displayed (Figure 2.7).
Page 71 Chapter 2 | Getting Started Figure 2.8 FileSets in GTYPE Data Tree You can create FileSets for any process where you need to select a file, for functions like: • Batch Analysis • Displaying analysis results • SNP Export • Pedigree Check •...
Page 72 Affymetrix GeneChip ® Genotyping Analysis Software User’s Guide To group files into a FileSet: Right-click the FileSets header in the Data Tree and select New FileSet from the shortcut menu. Figure 2.9 FileSets header in Data Tree Or, from the main menu, select Tools File Sets.
Page 73 Chapter 2 | Getting Started Select files in the Data Tree to create a file set and drag them to the FileSet Members box (Figure 2.11). Figure 2.11 Selecting files for a GTYPE FileSet To remove a file from the FileSets dialog box: Select the file in the FileSet Members list.
Page 74 Affymetrix GeneChip ® Genotyping Analysis Software User’s Guide To delete files from the fileset: Selecting the file in the FileSet Members List. Click the Remove Member button Click Save to save the edited FileSet. To rename a fileset: Right-click it in the Data Tree and select Rename FileSet from the shortcut menu.
Page 75 Chapter 2 | Getting Started OPENING CELL INTENSITY OR ANALYSIS RESULTS DATA You are able to display any data by using the open command. Each data has its own display, depending upon file type (cell intensity, analysis results, or report) and assay type (MPAM, DM, BRLMM mapping analysis, or GenFlex Tag).
Page 76 Affymetrix GeneChip ® Genotyping Analysis Software User’s Guide Figure 2.14 Open dialog box Select Experiments from the Data of Type drop-down list. Select the experiment of interest in the Experiments list. Click the OK button. The main display area displays information about the selected experiment in the Experiments window.
Page 77 Chapter 2 | Getting Started Figure 2.15 Experiments window The Experiment window provides a convenient way to review the attributes assigned to a sample or experiment. For more information, see Setting Up Sample Attributes, on page 182 CHANGING THE NAME OF A PROJECT, SAMPLE, EXPERIMENT OR FILESET You can change the name of a project, sample, experiment, or file set in the data tree.
Page 78 Affymetrix GeneChip ® Genotyping Analysis Software User’s Guide Figure 2.16 Rename Experiment dialog box Enter the new name in the New Name textbox. Click OK. The selected item is renamed. OPENING A REPORT GTYPE generates algorithm and SNP reports providing additional information about mapping analysis.
Page 79 Chapter 2 | Getting Started Figure 2.17 Open dialog box In the Data of Type drop-down list, choose Reports (*.rpt). Double-click the report you want to view, or select multiple reports and click Open. The report is displayed. If multiple reports are open, click the Reports button in the Shortcut Bar/Tools menu to view the next report.
Page 80: Shortcut Bar
Affymetrix GeneChip ® Genotyping Analysis Software User’s Guide Shortcut Bar The shortcut bar provides quick alternatives to menu bar commands; the shortcut buttons enable you to navigate between all of the open file types in the main display area. The shortcut bar has two sections: •...
Page 81 Chapter 2 | Getting Started SHORTCUT BAR - TOOLS The buttons displayed in the Tools shortcut bar depend on the types of files that are open. If no files are open, the following buttons are available: • File Sets • Virtual Sets •...
Page 82 Affymetrix GeneChip ® Genotyping Analysis Software User’s Guide Displays experiment information Displays an open cell intensity image Displays the FileSet Tool Opens the Virtual Set Definition window Opens the SNP Export tool Opens the Pedigree Check tool Opens the Sample Mismatch Report tool Figure 2.18 Shortcut Bar - top half...
Page 83 Chapter 2 | Getting Started Opens BRLMM Batch Analysis window Opens Batch Analysis Opens the Attribute Importer tool Opens the Add Cell Files dialog box to select data to display in the Probe Intensity window or display an open Probe Intensity window Displays an open Universal Tag window Displays an open Dynamic Modeling Mapping Analysis...
Page 84: Status Log
Affymetrix GeneChip ® Genotyping Analysis Software User’s Guide SHORTCUT BAR - SETTINGS Opens the Defaults dialog box Opens the Filter dialog box Opens the Mapping Algorithm Settings dialog box Figure 2.20 GTYPE Shortcut bar, Settings Status Log The status log displays system status messages. •...
Page 85 Working with Images Chapter...
Page 86 Chapter...
Page 87: Working With Images
Working with Images This chapter explains how to view a cell intensity image and how to: • Adjust the image settings for optimum viewing (see page 84) • View probe cell data (see page 89) • Highlight a probe set or selected probes in the image (see page 92) •...
Page 88 Affymetrix GeneChip ® Genotyping Analysis Software User’s Guide Main display area Figure 3.1 Drag cell intensity files to the main display area (GTYPE) Each cell intensity data file is displayed in an Image window (Figure 3.2).
Page 89 Chapter 3 | Working with Images Image window task bar Figure 3.2 Cell intensity data in the image window (GTYPE) The Image window displays the file name in the upper left corner (same as the experiment name entered during experiment setup in the ®...
Page 90 Affymetrix GeneChip ® Genotyping Analysis Software User’s Guide Figure 3.3 Cell intensity images, cascade view (top), tiled view (bottom)
Page 91 Chapter 3 | Working with Images If you change the view in the main display area to other file types, click the Image Views button in the shortcut bar to display the open cell intensity data. COMMANDS IN THE IMAGE WINDOW TASK BAR Auto Automatically scales the intensity of the current image based on the range of intensity levels in a selected region of the image.
Page 92: Adjusting The Image Settings
Affymetrix GeneChip ® Genotyping Analysis Software User’s Guide Adjusting the Image Settings You can adjust the image settings (intensity range, color, coordinates, and highlights) for the current image only or globally for all subsequently opened files. The image setting adjustments are described in the following sections: •...
Page 93 Chapter 3 | Working with Images Figure 3.4 Image Settings dialog box for the active file (left); Defaults dialog box, Image Settings tab for global settings (right) The following section describes how to find and set global settings. MAKING GLOBAL ADJUSTMENTS TO SUBSEQUENTLY OPENED IMAGES To adjust the global settings: •...
Page 94 Affymetrix GeneChip ® Genotyping Analysis Software User’s Guide SETTING THE INTENSITY RANGE You can enter a new lower or upper limit for the intensity range associated with an image and apply this subset of the dynamic range to the image. Lowering the upper limit increases the image brightness and raising the lower limit decreases the brightness.
Page 95 Chapter 3 | Working with Images Table 3.1 Color options for cell intensity data To Display... In the Image Settings or Defaults dialog box, choose the... A gray scale or pseudo color bar Color Bar option at the top of the Image window...
Page 96 Affymetrix GeneChip ® Genotyping Analysis Software User’s Guide SPECIFYING HIGHLIGHT COLORS You can specify highlighting colors for the grid or highlighted probe array cells (features). Click Highlights in the Image Settings or Defaults dialog box (Figure 3.4). The Highlight Colors dialog box opens (Figure 3.5).
Page 97: Viewing Probe Cell Data
Chapter 3 | Working with Images Custom color Luminosity scale field Figure 3.6 Color palette, custom color field displayed To select a predefined color, click one of the basic colors. To define a custom color, click Define Custom Colors, then use the click-and-drag method to move the cross hairs in the custom color field.
Page 98 Affymetrix GeneChip ® Genotyping Analysis Software User’s Guide The probe cell data is displayed. The type of information is different, depending upon which assay type is displayed: Mapping arrays (see Probe Cell Data: Mapping Arrays below) ® GenFlex Tag Mapping Array (see Probe Cell Data: ®...
Page 99 Chapter 3 | Working with Images Target Base The expected nucleotide at the position that corresponds to the substitution position of the probe sequence. Probe Base The actual nucleotide located at the substitution position of the probe sequence. Position Specifies a probe pair in the probe set. Tile Identifier for the probe set PROBE CELL DATA: GENFLEX...
Page 100: Viewing Probe Set Intensity Data
Affymetrix GeneChip ® Genotyping Analysis Software User’s Guide Viewing Probe Set Intensity Data You can highlight user selected probes sets in the cell intensity image. This is a convenient way to quickly view the cell intensities of probe sets of interest. You can also view cell intensities for probe sets on mapping arrays in the Probe Intensity Window.
Page 101 Chapter 3 | Working with Images Figure 3.9 View Probe Tiling dialog box, Features tab Selecting a probe set highlights different features in the different types of arrays: - Mapping array: Displays the probe cells used to call a particular SNP. - GenFlex Tag array: Displays the probe cells used for a selected tag.
Page 102 Affymetrix GeneChip ® Genotyping Analysis Software User’s Guide Figure 3.10 Highlighted fragment in the cell intensity image SELECTING PROBE SETS BY POSITION AND TILE NUMBER You can select the probe sets that you want to highlight by position and tile number: Right-click the cell intensity data and select View Probe Tiling in the shortcut menu, or select View Probe Tiling from the...
Page 103 Chapter 3 | Working with Images Figure 3.11 View Probe Tiling dialog box, Positions tab Click the Positions tab. Choose a position option: - Choose All Positions to highlight all positions of the selected tile(s). - Choose Position Number and enter the position number of interest.
Page 104 Affymetrix GeneChip ® Genotyping Analysis Software User’s Guide Mapping Arrays In mapping arrays, the tile value is an identifier for the probe set. The position value specifies a probe pair in the probe set. ® GenFlex Tag Arrays In GenFlex Tag arrays, the position value is the identifier for the probe set.
Page 105 Chapter 3 | Working with Images Figure 3.12 Click a highlighted feature to display the probe cell data To place the red cross hairs over the next feature of the highlighted probe set, click the image (to return focus to the Image window) and do one of the following: - Right-click the image and select View Next Highlight in the shortcut menu.
Page 106: Bookmarks
Affymetrix GeneChip ® Genotyping Analysis Software User’s Guide To return the cross hairs to a previous feature, do one of the following: - Right-click the image and select View Previous Highlight in the shortcut menu. - Select View Previous Highlight from the menu bar. To remove all highlights, do one of the following: - Right-click the image and select Clear Highlights from the shortcut menu.
Page 107 Chapter 3 | Working with Images CREATING A BOOKMARK To view an image area of interest at the desired magnification level, use the Image window task bar commands and scroll bars. Right-click the image and select View Bookmarks Bookmark from the shortcut menu, or select View Bookmarks Add Bookmark from the menu bar.
Page 108 Affymetrix GeneChip ® Genotyping Analysis Software User’s Guide EDITING A BOOKMARK Right-click the image and select View Bookmarks Edit Bookmarks from the shortcut menu, or select View Bookmarks Edit Bookmarks from the menu bar. The Edit Bookmarks dialog box opens (Figure 3.14).
Page 109: Default Image Settings
Chapter 3 | Working with Images Default Image Settings The default image settings functions are described in the sections below: • Viewing Default Settings (see below) • Changing the Intensity Range (see page 102) • Changing the Color Display (see page 102) •...
Page 110 Affymetrix GeneChip ® Genotyping Analysis Software User’s Guide • Analysis Defaults, on page 135 • Starting GTYPE, on page 50 The image settings specified in the Defaults dialog box (except for the color option) are applied to subsequently opened cell intensity data and do not affect an active, open file.
Page 111 Chapter 3 | Working with Images Highlight Colors You may specify new highlighting colors for the grid, masked cells, outlier cells, or highlighted probe array cells (features). Click Highlights in the Defaults dialog box (Figure 3.15). The Highlight Colors dialog box opens (Figure 3.16).
Page 112 Affymetrix GeneChip ® Genotyping Analysis Software User’s Guide Custom color Luminosity Figure 3.17 Color palette, custom color field displayed To select a predefined color, click one of the basic colors. To define a custom color, click Define Custom Colors, then use the click-and-drag method to move the cross hairs in the custom color field.
Page 113 Analyzing Cell Intensity Data Chapter...
Page 114 Chapter...
Page 115: Analyzing Cell Intensity Data
Analyzing Cell Intensity Data GTYPE provides several options for analyzing cell intensity data from DNA arrays. This chapter provides an overview of these options (see below) and instructions for performing an analysis using: • The Analyze dialog box (see page 110) •...
Page 116 Affymetrix GeneChip ® Genotyping Analysis Software User’s Guide GENERAL STEPS While you have several options for performing an analysis, you always follow the same basic steps: Select the assay type, using the Filters dialog box (see page 53). You can analyze mapping data from different types of arrays at the same time.
Page 117 Chapter 4 | Analyzing Cell Intensity Data MPAM Algorithm ® For the Affymetrix GeneChip Mapping 10K Array, an analysis is performed using the Modified Partitioning Around Medoids (MPAM) modeling algorithm. GTYPE uses the resulting cell intensity data to determine the genotype of the SNPs represented in the sample. The analysis results can be displayed in the MPAM mapping analysis window (see Chapter 5, Mapping Analysis Window, on page...
Page 118: Using The Analyze Dialog Box
Affymetrix GeneChip ® Genotyping Analysis Software User’s Guide page 335 Appendix D, Bayesian Robust Linear Model with Mahalanobis (BRLMM) Distance Classifier Algorithm (see page 353). ® GenFlex Tag Analysis ® For GenFlex Tag assays, GTYPE uses the cell intensity data from an Affymetrix GenFlex Tag array to determining the intensity for different tags.
Page 119 Chapter 4 | Analyzing Cell Intensity Data The Analyze dialog box opens (Figure 4.1). Click to display Filter options View buttons Figure 4.1 Analyze dialog box The Analyze dialog box provides several options for displaying cell intensity data files: - Click the View Details button to display the following information about each file: Data Name...
Page 120 Affymetrix GeneChip ® Genotyping Analysis Software User’s Guide Figure 4.2 Analyze dialog box with Filter categories displayed The Filter categories in the Analyze dialog box are identical to the categories in the Filters dialog box, described page 60, except that Date categories are not available.
Page 121 Chapter 4 | Analyzing Cell Intensity Data For mapping analyses only: - If you selected one file, the algorithm report is automatically assigned the name of the selected cell intensity data file and given the .rpt file extension. - If you selected more than one file, the algorithm report is assigned the name of the first cell intensity data file in the list and given the .rpt file extension.
Page 122: Using The Data Tree
Affymetrix GeneChip ® Genotyping Analysis Software User’s Guide If you don’t want to overwrite previously generated analysis results files or algorithm reports, click and use the Batch Analysis window to perform the analysis (see Using the Batch Analysis ) or change the name of the file in the Save Window, on page 117 Results As dialog box.
Page 123 Chapter 4 | Analyzing Cell Intensity Data You may need to set certain parameters, depending upon the type of analysis you are performing. For more information, see Changing Algorithm Settings, on page 128 In the data tree, select the cell intensity data files that you want to analyze, right-click the selection, and click Analyze in the shortcut menu (MPAM and DM only).
Page 124 Affymetrix GeneChip ® Genotyping Analysis Software User’s Guide If you are going to overwrite a previously generated analysis results file, a warning box opens (Figure 4.6). Figure 4.6 Overwrite warning dialog box - Click Yes to continue the analysis. If you don’t want to overwrite previously generated analysis results files or algorithm reports, click NO and use the Batch Analysis window to perform the analysis (see Using the Batch Analysis...
Page 125: Using The Batch Analysis Window
Chapter 4 | Analyzing Cell Intensity Data Using the Batch Analysis Window The Batch Analysis window provides a convenient way to: • See the cell intensity data selected for analysis • See the analysis results files and the report that will be generated •...
Page 126 Affymetrix GeneChip ® Genotyping Analysis Software User’s Guide To open the Batch Analysis window: • Click the appropriate Batch Analysis shortcut button ; or, Select Run Batch Analysis from the menu bar. The Batch Analysis window opens (Figure 4.8). Figure 4.8 Batch Analysis window in GTYPE...
Page 127 Chapter 4 | Analyzing Cell Intensity Data BATCH ANALYSIS WINDOW TOOLBAR The Batch Analysis window toolbar (Figure 4.9) provides quick access to the commonly used functions of the window. Figure 4.9 Batch Analysis window toolbar You can display toolbars with text labels. To display the toolbar button labels, select View Toolbar Text Labels from the menu...
Page 128 Affymetrix GeneChip ® Genotyping Analysis Software User’s Guide RUNNING AN ANALYSIS To analyze intensity data using the Batch Analysis Window: Select the assay type, using the Filters dialog box (see page 53). Make any desired changes to the algorithm parameters (see page 128).
Page 129 Chapter 4 | Analyzing Cell Intensity Data Figure 4.10 Add Cell/Chip data items dialog box View options and Filter categories provide several alternatives for displaying file information (see page 111). Select the cell intensity data files that you want to analyze and click Open.
Page 130 Affymetrix GeneChip ® Genotyping Analysis Software User’s Guide MPAM mapping array data Dynamic Model mapping array data Dynamic Model mapping array data cell intensity data analysis results files report files selected for the analysis (*.chp) Figure 4.11 Batch Analysis window with data from different mapping arrays selected for analysis To remove cell intensity data from the Batch Analysis window: - Select the cell intensity data files and click the Remove button...
Page 131 Chapter 4 | Analyzing Cell Intensity Data Click the Analyze toolbar button ; or Select Edit Start Analysis from the menu bar. If you are going to overwrite previously generated analysis results files, a warning box opens (Figure 4.12). Figure 4.12 Overwrite warning dialog box - Click Yes to continue the analysis.
Page 132 Affymetrix GeneChip ® Genotyping Analysis Software User’s Guide • Rename selected analysis results files in the Batch Analysis window (see page 125) Renaming Analysis Results Files Automatically The Batch Analysis window provides a convenient way to modify the results file names. In the Batch Analysis Options dialog box, you can specify a prefix or suffix that is automatically added to the cell file names.
Page 133 Chapter 4 | Analyzing Cell Intensity Data The prefix and suffix are applied to all of the analysis results file names when cell intensity data files are subsequently added to the Batch Analysis window. Analysis results file names for cell intensity data added to the Batch Analysis window before selecting a prefix and/or suffix will not be renamed.
Page 134 Affymetrix GeneChip ® Genotyping Analysis Software User’s Guide To edit a single file name in the Batch Analysis window, do one of the following: • Double-click the file name and edit the name, or • Select the file name that you want to edit, select Edit Rename Output File from the menu bar, and edit the results file name.
Page 135 Chapter 4 | Analyzing Cell Intensity Data toolbar Figure 4.15 Export File List dialog box The dialog box toolbar provides standard options for selecting directories and displaying the list of files. Enter a name for the file list (*.txt) and click Save. Importing a File List To import a file list: Click the Batch Analysis shortcut button...
Page 136: Changing Algorithm Settings
Affymetrix GeneChip ® Genotyping Analysis Software User’s Guide toolbar Figure 4.16 Import File List dialog box The dialog box toolbar provides standard options for selecting directories and displaying the list of files. Double-click the file list that you want to import. The cell intensity data files, analysis results files, and reports in the file list, including the file pathways, are added to the Batch Analysis window.
Page 137 Chapter 4 | Analyzing Cell Intensity Data MPAM MAPPING ALGORITHM SETTINGS For best performance, you should assign a gender to the sample when registering the experiment and enter values for gender attributes in GTYPE. For more information, see Using the Gender Attribute Values, on page 130 Determining Sample Gender, on page 328 To view the user-modifiable algorithm settings:...
Page 138 Affymetrix GeneChip ® Genotyping Analysis Software User’s Guide The parameters for that array type are displayed. Click the item you want to change. The current value for the item is displayed (Figure 4.17). Enter a new value for the item. To return all settings to the factory set defaults, click Default.
Page 139 Chapter 4 | Analyzing Cell Intensity Data Other attribute data can be imported into GTYPE and used for different analyses (for more information, see Setting Up Sample Attributes, on page 182 To define the gender attribute and values: In GCOS, specify a gender attribute and a controlled vocabulary for values in the Sample template you will use for your experiments (Figure 4.18).
Page 140 Affymetrix GeneChip ® Genotyping Analysis Software User’s Guide See the GCOS user manual for more information about specifying and assigning attributes. In GTYPE, enter the parameter name and values used in the Sample template in the appropriate places in the Mapping Algorithm Settings dialog box.
Page 141 Chapter 4 | Analyzing Cell Intensity Data To change a setting: Select the array type you are analyzing from the Probe Array Type drop-down box. The parameters for that array type are displayed. Click the item you want to change. The current value for the item is displayed (Figure 4.20).
Page 142 Affymetrix GeneChip ® Genotyping Analysis Software User’s Guide Select array type here Enter a new value for the selected item here Figure 4.21 Mapping Algorithm Settings dialog box, Dynamic Model mapping settings displayed To change a setting: Select the array type you are analyzing from the Probe Array Type drop-down box.
Page 143: Analysis Defaults
Chapter 4 | Analyzing Cell Intensity Data Linear Model with Mahalanobis (BRLMM) Distance Classifier Algorithm, on page 353. Analysis Defaults The Analysis Settings tab (Figure 4.22) on the Defaults dialog box displays two options that are available when an analysis is run. Figure 4.22 Analysis Settings tab in the Defaults window PROMPT FOR OUTPUT DATA NAME...
Page 144 Affymetrix GeneChip ® Genotyping Analysis Software User’s Guide DISPLAY SETTINGS WHEN ANALYZING DATA Choose the Display settings when analyzing data option to display the appropriate Algorithm Settings dialog box at the start of an analysis (Figure 4.22).
Page 145 Mapping Analysis Window Chapter...
Page 146 Chapter...
Page 147: Mapping Analysis Window
Mapping Analysis Window This chapter describes the Mapping Analysis Window, which displays results of sample analyses using the MPAM, DM, and BRLMM mapping analysis tools. This chapter includes: Mapping Analysis Window • Overview • Features • Displaying Results • Genotype Calls •...
Page 148: Features
Affymetrix GeneChip ® Genotyping Analysis Software User’s Guide When the CHP data is opened in GTYPE, the mapping analysis window opens automatically to display the SNP information (Figure 5.1). Mapping Analysis Window Figure 5.1 Mapping Analysis Window Features In the mapping analysis window you can: •...
Page 149: Displaying Results In The Mapping Analysis Window
Chapter 5 | Mapping Analysis Window • Perform Loss of Heterozygosity studies between selected arrays (see page 247) • Sort the SNP Table (see page 157) • Search the table for a text string (see page 158) • Export content from the table (see page 159) •...
Page 150 Affymetrix GeneChip ® Genotyping Analysis Software User’s Guide To select adjacent files, press and hold the Shift key while you click the first and last file in the selection. To select non-adjacent files, press and hold the Ctrl key while you click the files. Right-click the selection and select Open in the shortcut menu.
Page 151 Chapter 5 | Mapping Analysis Window Sample Project Category used to group samples, assigned in GCOS. Sample Type Additional description of the sample, assigned in GCOS. Click the View List button to display only the name of the available files. You can also use the Filter categories to display only files that meet certain criteria (Figure...
Page 152 Affymetrix GeneChip ® Genotyping Analysis Software User’s Guide The analysis data results that match the selected categories is displayed in the dialog box. Select the CHP data files that you want to view and click OK. The window displays the selected results (Figure 5.4) in the mapping analysis window.
Page 153 Chapter 5 | Mapping Analysis Window You can display toolbars with text labels. To display the toolbar button labels, select View Toolbar Text Labels from the menu bar. Table 5.1 Mapping Analysis Window – toolbar button functions Menu Bar Command Toolbar Function Button...
Page 154: Mapping Analysis - Genotype Calls
Affymetrix GeneChip ® Genotyping Analysis Software User’s Guide Mapping Analysis – Genotype Calls The MPAM, DM, and BRLMM mapping analysis results in the following genotype calls displayed in the mapping analysis window: • AA call • AB call • BB call •...
Page 155 Chapter 5 | Mapping Analysis Window Allele calls are made for a sample by comparing its sense and antisense strand RAS values to a SNP model, created using Modified Partitioning Around Medoids (MPAM), in the mapping algorithm. Each SNP in the model has medoids defined for the AA, AB, and BB alleles (Figure 5.6).
Page 156 Affymetrix GeneChip ® Genotyping Analysis Software User’s Guide DM – CONFIDENCE SCORE The DM Rank score is an indication of the probability that the SNP can be assigned to a particular genotype. The smaller the rank score, the larger the probability that the call is correct. Each SNP has a rank score for: •...
Page 157: Snp Table
Chapter 5 | Mapping Analysis Window SNP Table When you open a CHP file (or drag and drop it) in the mapping analysis window, the lower half of the window displays a table that lists SNP information for the specific analysis performed (MPAM, DM, or BRLMM).
Page 158 Affymetrix GeneChip ® Genotyping Analysis Software User’s Guide Columns of Sample Data SNP ID NetAffx Genotype Call Zone Genotype Call Zone Annotation Call Score Score Call Figure 5.7 Example of an MPAM SNP Table Columns of Sample Data Default NetAffx Annotation Genotype Confidence...
Page 159 Chapter 5 | Mapping Analysis Window Columns of Sample Data Default NetAffx SNP ID Annotation Genotype Genotype Confidence Call Call Score Figure 5.9 Example of a BRLMM SNP Table SNP TABLE FEATURES • Hide or display selected columns • Sort the data in the table by one or more columns (see page 157) •...
Page 160 Affymetrix GeneChip ® Genotyping Analysis Software User’s Guide SNP TABLE – DISPLAY OPTIONS Table Tab By default, only the sample data Genotype Call and Confidence Score (DM and BRLMM) or Call Zone Score (MPAM) are displayed in the table. You can display other columns by selecting the options on the Table tab in the Mapping Analysis Options box (View Options Settings)Figure...
Page 161 Chapter 5 | Mapping Analysis Window NetAffx™ Tab To set NetAffx options, select the NetAffx User Account Information tab in the Mapping Analysis Options dialog box. The user name and password are not required for most annotations and will be empty. See Setting the Advanced Options (page 285).
Page 162 Affymetrix GeneChip ® Genotyping Analysis Software User’s Guide To view the Display tab: Click the Options button The Mapping Analysis Options dialog box opens. Click the Display tab to view display options Click Defaults to return all settings to the default values. Figure 5.12 Display tab showing DM values The first time you choose to display data for an array type in the...
Page 163 Chapter 5 | Mapping Analysis Window SNP TABLE – COLUMN DEFINITIONS Sample ID An ID used for the sample. When combining array sets in a virtual array, the Sample ID is made by concatenating the values for the sample attributes used to define the virtual array. Displaying Data in Virtual Arrays, on page 193.
Page 164 Affymetrix GeneChip ® Genotyping Analysis Software User’s Guide • Right-click in the table and select Show All Columns from the shortcut menu. You can also use the Analysis Options dialog box to display or hide all columns of a particular data type: Click the Options button The Mapping Analysis Options dialog box opens (Figure...
Page 165 Chapter 5 | Mapping Analysis Window SORTING THE SNP TABLE Single Column Table Sort You can sort the table on any data column in ascending or descending order. To sort on a single column: • Right-click the column header of interest and click Sort Ascending or Sort Descending in the shortcut menu.
Page 166 Affymetrix GeneChip ® Genotyping Analysis Software User’s Guide Figure 5.15 Sort dialog box To specify a second sort, click the drop-down arrow in the next Then By box, select a data column from the drop-down list, and select the Ascending or Descending sort order. To specify another sort, repeat step 3.
Page 167 Chapter 5 | Mapping Analysis Window Figure 5.16 Find dialog box Enter the text string for the search (up to 256 alphanumeric characters). Choose the Match entire cell text option to find an exact match for the search string in a cell. If the option is selected, the text in a cell must completely agree with the text in the dialog box.
Page 168 Affymetrix GeneChip ® Genotyping Analysis Software User’s Guide You can also export mapping analysis data in formats that can be used by different analysis software (see Exporting Data with the SNP Export Tool, on page 226 If you export the complete set of data for a pair of arrays in a virtual set, you will not be able to open the resulting file in Microsoft Excel because the number of rows exceeds Excel’s maximum.
Page 169 Chapter 5 | Mapping Analysis Window toolbar Figure 5.17 Export Table dialog box The dialog box toolbar provides standard options for selecting directories and displaying the list of files. Select a directory for the file or use the default directory. Enter a name for the *.txt file.
Page 170 Affymetrix GeneChip ® Genotyping Analysis Software User’s Guide Copying the Table All or part of the table can be copied to the system clipboard and pasted into other applications. To select the entire table: • Click the upper left corner of the table (Figure 5.18).
Page 171 Chapter 5 | Mapping Analysis Window To select non-adjacent rows (or columns): • Press and hold the Ctrl key while you click the rows (columns). To copy the selection to the system clipboard, do one of the following: • Click the Copy Cells button •...
Page 172: Scatter Plots
Affymetrix GeneChip ® Genotyping Analysis Software User’s Guide In the Print Range section, select the Table checkbox. Select the All or Selection radio button. - All prints out all of the rows that will fit on a single printed page. - Selection prints out the selected rows in the table.
Page 173 Chapter 5 | Mapping Analysis Window Tool Bar RAS Scatter Plot SNP Table Figure 5.20 MPAM scatter plot in the mapping analysis window...
Page 174 Affymetrix GeneChip ® Genotyping Analysis Software User’s Guide Relative Allele Signals (RAS) For a selected SNP, the RAS Scatter Plot (Figure 5.21) displays: • The medoids and call zone radii for the SNP model used to make the allele call •...
Page 175 Chapter 5 | Mapping Analysis Window color. If the sample does not have an allele call, it is displayed in a fourth color. For SNPs on the X chromosome, you may see discrepancies between a SNP’s actual status as called or not called in the SNP table and its relationship to the displayed model medoids and call zones in the Scatter Plot for the following reason: If the sample is not assigned to a gender by the experimenter, SNPs on...
Page 176 Affymetrix GeneChip ® Genotyping Analysis Software User’s Guide DM SCATTER PLOT When you open a CHP file resulting from DM analysis, the mapping analysis window displays a DM scatter plot (Figure 5.22) in the top half of the window for the selected SNP. This is a plot of rank scores for each sample.
Page 177 Chapter 5 | Mapping Analysis Window AB Confidence scores No Call Confidence scores rank score BB Confidence thresholds AA Confidence scores scores Figure 5.23 DM Scatter Plot The symbol and color depend on the genotype calls. The plot also displays the threshold value for the calls. Both the symbol/color and threshold values are user adjustable.
Page 178 Affymetrix GeneChip ® Genotyping Analysis Software User’s Guide SNP Call Figure 5.24 SNP call – right-click for information pop-up SELECTING ITEMS FOR DISPLAY IN THE SCATTER PLOT Selecting a SNP for Display To select a SNP for display: • Click anywhere in the SNP’s row in the table. You can also step sequentially through the SNPs by using the Step or Step Down buttons.
Page 179 Chapter 5 | Mapping Analysis Window Figure 5.25 Print dialog box The Print dialog box includes the standard Windows print options (select printer, change properties, number of copies, etc., depending upon your system and printer). In the Print Range section, select the Graph checkbox. Click OK.
Page 180 Affymetrix GeneChip ® Genotyping Analysis Software User’s Guide CHANGING THE SCATTER PLOT DISPLAY OPTIONS The Display tab of the MPAM or DM Mapping Analysis Options dialog box allows you to control the display of the Scatter Plot: • Call threshold - Turn the display of the radii (MPAM) or the threshold (DM) on and off - Change the call zone radius (MPAM)or the call threshold (DM)
Page 181 Chapter 5 | Mapping Analysis Window Figure 5.26 MPAM Mapping Analysis Options Controlling the Display of Call Zones (MPAM) The Show Call Zone Radius checkbox allows you to turn the display of the Call Zone on or off. The Call Zone Radius box allows you to display confidence contours for different call zone radius values.
Page 182 Affymetrix GeneChip ® Genotyping Analysis Software User’s Guide Figure 5.27 Dynamic Model Mapping Analysis Options Controlling the Display of Call Thresholds (DM) The Show Call Threshold allows you to turn the display of the rank score threshold on or off. The Call Threshold box allows you to change the displayed rank score threshold.
Page 183 Chapter 5 | Mapping Analysis Window Select or deselect the Show Call Threshold checkbox. Click the OK button. Displaying Only Highlighted Values You can turn off the display of the RAS values (MPAM) or SNP calls (DM) for unhighlighted samples using the Show Highlight Only checkbox.
Page 184 Affymetrix GeneChip ® Genotyping Analysis Software User’s Guide Figure 5.28 Call Types menu To change the display of call types: Click the color swatch for the feature you want to change: The color palette opens. Custom color Luminosity scale Figure 5.29 Color palette, custom color field displayed...
Page 185 Chapter 5 | Mapping Analysis Window To select a predefined color, click a basic color. To define a custom color, click Define Custom Colors and use the click-and-drag method to move the cross hairs in the custom color field. Adjust the color brightness using the luminosity scale to the right.
Page 186 Affymetrix GeneChip ® Genotyping Analysis Software User’s Guide...
Page 187 Working with Mapping Data Chapter...
Page 188 Chapter...
Page 189: Working With Mapping Data
Working with Mapping Data You can assign a sample ID and other attributes, such as gender and pedigree information to the samples analyzed in GTYPE, using GCOS sample templates (see page 182) and the AttributeImporter Tool (see page 185). Doing this allows you to use several tools for further analysis of the mapping data.
Page 190: Setting Up Sample Attributes
Affymetrix GeneChip ® Genotyping Analysis Software User’s Guide Setting Up Sample Attributes To import sample attributes and use the pedigree data tools, you must: • Set up a sample template with attributes for pedigree data in GCOS Manager (see below) •...
Page 191 Chapter 6 | Working with Mapping Data Attributes include information like: • Sample ID • Family ID • Father ID • Mother ID • Gender • Disease State To create an attribute for a template, you define: • Attribute name •...
Page 192 Affymetrix GeneChip ® Genotyping Analysis Software User’s Guide The Experiments window provides a convenient way to review the sample attribute values for a selected experiment. For more information, see Experiments Window, on page 67 See Chapter 15, GCOS Manager, in the Affymetrix GeneChip ®...
Page 193: Importing Pedigree/Attribute Information
Chapter 6 | Working with Mapping Data When you select a sample template from the drop-down list, the attributes for that template appear in the window. After you have registered the sample and defined the experiment, the GCOS process database will allow you to import the attributes. ®...
Page 194 Affymetrix GeneChip ® Genotyping Analysis Software User’s Guide CREATING THE DATA FILE The data file (Figure 6.3) is a tab-delimited text file containing the sample data to be imported. The file can be created by a database export or entered using a spreadsheet or text editor and should be saved in tab-delimited text format.
Page 195 Chapter 6 | Working with Mapping Data Figure 6.4 AttributeImporter Tool window The AttributeImporter Tool allows you to: - Select the data file for import - Select the attributes in the data file - Select options for the import Click Browse. The Open dialog box opens (Figure 6.5).
Page 196 Affymetrix GeneChip ® Genotyping Analysis Software User’s Guide Figure 6.5 Select File dialog box Use the dialog box toolbar to locate and select the data file. Click Open. The path and data file name appear in the textbox. The attributes and their column assignments appear in the table (Figure 6.6).
Page 197 Chapter 6 | Working with Mapping Data Data in Sex column of the data file is assigned to Gender attribute in the sample template Figure 6.6 AttributeImporter Tool with attributes displayed The table contains the following columns: Header Labels Header for a column in the sample data file (cannot be edited). Attribute Attribute in the sample template assigned to the header (can be edited).
Page 198 Affymetrix GeneChip ® Genotyping Analysis Software User’s Guide Select options for the import. - Select the Modify Existing Samples checkbox to modify attribute values for samples already present in the database. - Select the Create New Samples check box to create a new placeholder sample if the sample is not previously found in the database.
Page 199 Chapter 6 | Working with Mapping Data Figure 6.7 Import notice - Click No to close the warning dialog box and return to the AttributeImporter Tool window, where you can edit the attribute name to match the sample template; or - Click Yes to proceed with the import and ignore the missing attribute.
Page 200 Affymetrix GeneChip ® Genotyping Analysis Software User’s Guide Figure 6.9 Log Notification Log messages also appear in the Status window. The log notification box tells you where to find the import log file (Figure 6.10). Figure 6.10 Log file The following information is reported for every sample processed: - Whether the sample was modified or created - Exceptions encountered during the import.
Page 201: Displaying Data In Virtual Arrays
Chapter 6 | Working with Mapping Data SECURITY ROLES FOR GCOS SERVER The AttributeImporter tool uses the standard security model used by GCOS and GCOS Manager. This model is controlled by the Roles tab in GCOS Manager. The following Roles are required for the operation specified: •...
Page 202 Affymetrix GeneChip ® Genotyping Analysis Software User’s Guide and last names. The social security number (SSN) is a single attribute that uniquely identifies a person. Alternately the first and last name together also uniquely identify the person. In the lab, a Sample ID could be used as a single attribute for this purpose, or the pedigree identifiers Family ID and Person ID.
Page 203 Chapter 6 | Working with Mapping Data For more information on sample templates and attributes see Setting Up Sample Attributes, on page 182. Grouping array data into virtual arrays requires two steps: Define a virtualset rule (see below). Apply the rule to a selection of array data (see page 199).
Page 204 Affymetrix GeneChip ® Genotyping Analysis Software User’s Guide Or, click the Virtual Sets button in the Genotyping Views shortcut bar. Or, select Tools VirtualSet from the menu bar. The VirtualSet Definition dialog box opens (Figure 6.13). Figure 6.13 VirtualSet Definition dialog box The dialog box is divided into the following sections: Specify VirtualSet Name: (see below) Select attributes uniquely identifying a sample: (see page 197)
Page 205 Chapter 6 | Working with Mapping Data Figure 6.14 Step 1 – Specify VirtualSet Name Virtualset Name Contains the name of the virtual array set. The virtual set name can be selected from previously saved sets, or a new name can be entered. Enter a name in the VirtualSet Name textbox;...
Page 206 Affymetrix GeneChip ® Genotyping Analysis Software User’s Guide Select the template used for the samples you wish to group from the Templates drop-down list. The attributes assigned to the template appear in the Template Attributes box. Also displayed is the special attribute “Sample Name.”...
Page 207 Chapter 6 | Working with Mapping Data You can remove array types by selecting them and clicking the << Remove button. You can remove all selected array types by clicking the << Remove All button. Click Save to save the Virtualset Definition. The definition is saved and can be used to group data.
Page 208 Affymetrix GeneChip ® Genotyping Analysis Software User’s Guide attribute values Figure 6.18 Virtual sets displayed in SNP table The sample ID in the SNP Table is created by concatenating the values for the attributes used to define the virtual arrays. The Experiments window provides a convenient way to review the sample attribute values for a selected experiment.
Page 209: Checking For Mendelian Inheritance Error
Chapter 6 | Working with Mapping Data Virtual sets are used to group data from the same sample run on multiple mapping arrays and are either displayed in the Mapping Analysis window or exported using the SNP Exporter tool. Note that while virtual sets can be created and data can be exported by combining any mapping array, the viewer cannot display 10K + 100K CHP data or 10K + 500K CHP data.
Page 210 Affymetrix GeneChip ® Genotyping Analysis Software User’s Guide To run the pedigree check: Click the Pedigree Check button in the Genotyping Views shortcut bar; or Select Tools Pedigree Check... from the menu bar. The Pedigree Check dialog box appears (Figure 6.19).
Page 211 Chapter 6 | Working with Mapping Data Figure 6.20 Specify sample attribute containing pedigree information Sample Attribute Displays sample templates and template attributes for Selection: selection. Template Name Drop-down list of the available templates. Template List of the attributes in the selected sample template. Attributes Person Unique identifier for the person from whom the sample was...
Page 212 Affymetrix GeneChip ® Genotyping Analysis Software User’s Guide Select the attribute used to identify the person from whom the sample was taken and click the Add >> button for the Family box. Select the attribute used to identify the family and click the Add >>...
Page 213 Chapter 6 | Working with Mapping Data Select the project, sample, experiments, or analysis data in the data tree and drag them to the Step 2 (Data) box. You may wish to use the Filter feature to display items of interest in the data tree (for more information, see Using the Filters Dialog Box, on page 60...
Page 214 Affymetrix GeneChip ® Genotyping Analysis Software User’s Guide dialog box toolbar Figure 6.23 Save As dialog box Use the dialog box toolbar to select a directory for the report file. Enter a name for the pedigree report in the File Name box. Click Save.
Page 215 Chapter 6 | Working with Mapping Data Figure 6.24 Mendelian Error report (displayed in spreadsheet software) The report can be displayed as a spreadsheet or in text editing software. Information for the SNPs and trios is displayed in the following columns: AffyID Unique identifier assigned to the SNP by Affymetrix Family...
Page 216: Using The Sample Mismatch Report Tool
Affymetrix GeneChip ® Genotyping Analysis Software User’s Guide Additionally, a summary of information about each family is also provided (Figure 6.25): Figure 6.25 Family Summary information Sample ID Unique identifier assigned to the person from whom the sample was taken. SNP Errors for the The total number of SNPs not satisfying Mendelian inheritance sample...
Page 217 Chapter 6 | Working with Mapping Data two individuals or samples. The averaged IBS metric, or Mismatch score, increases with the relatedness of the pair: • Identical twins and samples from the same person should have Mismatch scores ranging from 1.95 to 2.0. •...
Page 218 Affymetrix GeneChip ® Genotyping Analysis Software User’s Guide Figure 6.26 Sample Mismatch report dialog box CHECKING FOR SAMPLE MATCHES To check for sample matches, you only need to select files for comparison. You do not need to specify sample template attributes. To run a sample match report: Open the Sample Mismatch Report dialog box.
Page 219 Chapter 6 | Working with Mapping Data Specify output file name. (see page 205) Drag and drop .chp files from the Data Tree. In this step you select the samples for the pedigree check (Figure 6.27). Figure 6.27 Selecting samples for Sample Match report Select the project, sample, experiments, or analysis data in the data tree and drag them to the Step 1 (Data) box.
Page 220 Affymetrix GeneChip ® Genotyping Analysis Software User’s Guide Specify the mismatch threshold for calling matched samples. Figure 6.28 Enter an Mismatch threshold value. Enter a value for the Mismatch threshold in the box (Figure 6.28). Sample pairs with Mismatch scores greater than this threshold will be flagged as belonging to the same person.
Page 221 Chapter 6 | Working with Mapping Data Enter the report name and path in the Report File Name textbox; or, click the Browse button.The Save As dialog box opens (Figure 6.30). dialog box toolbar Figure 6.30 Save As dialog box 1.
Page 222 Affymetrix GeneChip ® Genotyping Analysis Software User’s Guide Figure 6.31 Report Completed dialog box Click Yes to display the report in Microsoft Notepad. If an error is identified by running the Sample Mismatch Report, fix the error and rerun the Sample Mismatch Report to confirm that there are no additional errors.
Page 223 Chapter 6 | Working with Mapping Data Header Legend Results Figure 6.32 Sample Match report opened in spreadsheet software The report can be displayed as a spreadsheet or in text editing software.
Page 224 Affymetrix GeneChip ® Genotyping Analysis Software User’s Guide Header The Header (Figure 6.33) lists basic information about the file: Figure 6.33 Sample Match report header Sample Mismatch Report type report Report File Name Identifier assigned in Sample Mismatch report dialog box. Date Date and time the report was generated.
Page 225 Chapter 6 | Working with Mapping Data Legend The Legends (Figure 6.34) explain the codes used in the report: Figure 6.34 Sample Match Report legend Mismatch Legend Defines the Mismatch scores and describes the thresholds. Mismatch Code Legend Defines person IDs and genders. Has Problem Legend Not applicable for sample match report.
Page 226 Affymetrix GeneChip ® Genotyping Analysis Software User’s Guide Results The Results (Figure 6.35) of the comparisons are listed below the legends: Figure 6.35 Sample Match Report results Mismatch Code Summary Numbers of different types of conflicts discovered. Comparison Results Listing of the chip comparisons with details of problems: Chp1 Chip 1 filename Chp2...
Page 227 Chapter 6 | Working with Mapping Data CHECKING FOR SAMPLE MISMATCHES The report is able to use sample attribute information to identify sample mismatches. The same steps are used as for the sample match report, and in addition, the sample attributes need to be specified in Step 3.
Page 228 Affymetrix GeneChip ® Genotyping Analysis Software User’s Guide Click the Define Sample Attributes button. The Sample Attribute Definition dialog box opens (Figure 6.37). Figure 6.37 Sample Attribute Definition dialog box The box displays the following controls: Sample Attribute Displays sample templates and template attributes for Selection: selection.
Page 229 Chapter 6 | Working with Mapping Data A list of the attributes associated with the selected template appears in the Template Attributes box. Select the attribute used to identify the person from whom the sample was taken and click the Add >> button for the Person box. Select the attribute used to identify the sex and click the Add >>...
Page 230 Affymetrix GeneChip ® Genotyping Analysis Software User’s Guide Header Legend Results Figure 6.38 Sample Mismatch report opened in spreadsheet software The report can be displayed as a spreadsheet or in text editing software.
Page 231 Chapter 6 | Working with Mapping Data Header The Header (Figure 6.39) lists basic information about the file: Figure 6.39 Sample Mismatch report header Sample Mismatch Report type report Report File Name Identifier assigned in Sample Mismatch report dialog box. Date Date and time the report was generated.
Page 232 Affymetrix GeneChip ® Genotyping Analysis Software User’s Guide Legend The Legends (Figure 6.40) explain the codes used in the report: Figure 6.40 Sample Mismatch Report legend Mismatch Legend Defines the Mismatch scores and describes the thresholds. Mismatch Code Lists the codes used to describe problems (see below). Legend...
Page 233 Chapter 6 | Working with Mapping Data Results The Results (Figure 6.41) of the comparisons are listed below the legends: Figure 6.41 Sample Mismatch Report results The report lists: • All sample pairs with mismatch (IBS) scores above the mismatch threshold •...
Page 234: Exporting Data With The Snp Export Tool
Affymetrix GeneChip ® Genotyping Analysis Software User’s Guide PerID 2 Sample ID 2 GCOSGen1 Gender in the GCOS database for Chip 1. GCOSGen2 Gender in the GCOS database for Chip 2. GTYPEeGen1 Gender called by GTYPE for Chip 1. GTYPEGen2 Gender called by GTYPE for Chip2.
Page 235 Chapter 6 | Working with Mapping Data • Merlin format Tab-delimited format exports the data into tab-delimited text files that can be displayed in Microsoft Notepad, Microsoft Excel, and other spreadsheet and text-editing software. Haploview format is used by the Haploview association analysis software.
Page 236 Affymetrix GeneChip ® Genotyping Analysis Software User’s Guide TYPES OF SNP OUTPUT FILES The SNP call data and pedigree data, if available, is exported in a set of files. You can select from the following types of SNP data files: •...
Page 237 Chapter 6 | Working with Mapping Data Table 6.1 Merlin File Formats Output Files Description Data Type File The data file includes one row per data item in the pedigree file, indicating the data type (encoded as M - marker, A - affection status, T - Quantitative Trait and C - Covariate) and providing a one-word label for each item.
Page 238 Affymetrix GeneChip ® Genotyping Analysis Software User’s Guide Quantitative Traits The GeneHunter open source software datafile contains the means and covariances for the traits. Dummy values are written by the application. The user has to edit the file with the correct values. Allele Frequencies ™...
Page 239 Chapter 6 | Working with Mapping Data Figure 6.42 SNP Export dialog box, Tab-delimited export selected The dialog box is divided into the following sections: - Step 1: Drag and Drop .chp files from the Data Tree (see below) - Step 2: Select SNP Filter Conditions (Optional) (see page 232) - Step 3: Select output options (see page 235)
Page 240 Affymetrix GeneChip ® Genotyping Analysis Software User’s Guide Figure 6.43 Selecting data in the Data Tree Select the project, sample, experiments, analysis data, or FileSets in the data tree and drag them to the Samples box. The associated mapping analysis data is displayed in the Samples box.
Page 241 Chapter 6 | Working with Mapping Data - Mendelian Error rate - SNP Call Rate Before using the Mendelian Error filter, you must: 1. Assign a sample template with pedigree attributes to the samples (see page 182) 2. Import sample attribute data (see page 185) Figure 6.44 Step 2: Select SNP Filter Conditions (Optional)
Page 242 Affymetrix GeneChip ® Genotyping Analysis Software User’s Guide Number of Errors Specify number of errors for filtering SNPs. per family Specify Pedigree Opens the Pedigree Information dialog box to select Information pedigree attributes (see below). To use the filters: Select the Filters and enter threshold values. To set the pedigree information, click the button.
Page 243 Chapter 6 | Working with Mapping Data Person Unique identifier for the person from whom the sample was taken. Family ID Unique identifier for the family. Father Unique identifier for the father. This field is blank (null) for founders (individuals whose parents are not known). Mother Unique identifier of the mother.
Page 244 Affymetrix GeneChip ® Genotyping Analysis Software User’s Guide Enter the path and file name in the Data Type File textbox; or Click Browse. The Save As dialog box opens (Figure 6.47). dialog box toolbar Figure 6.47 Save As dialog box Use the dialog box toolbar to locate the directory and enter the file name.
Page 245 Chapter 6 | Working with Mapping Data EXPORTING DATA FOR ASSOCIATION AND LINKAGE ANALYSIS SOFTWARE Before exporting data for linkage analysis, you must: 1. Assign a sample template with pedigree attributes to the samples (see page 182) 2. Assign sample attribute data (see page 185) To export data for association and linkage analysis: Click the SNP Export button...
Page 246 Affymetrix GeneChip ® Genotyping Analysis Software User’s Guide Figure 6.48 SNP Export dialog box, Merlin format selected The dialog box is divided into the following sections: - Step 1: Specify sample attributes containing pedigree information (see below) - Step 2: Select samples to export.
Page 247 Chapter 6 | Working with Mapping Data Specify sample attributes containing pedigree information In this step you specify the sample attributes containing the pedigree information of interest (Figure 6.49). Figure 6.49 Sample attributes for Merlin and Haploview export Sample Attribute Selection: Template Name Drop-down list of the available templates.
Page 248 Affymetrix GeneChip ® Genotyping Analysis Software User’s Guide The following features apply only to GeneHunter open source software (Figure 6.50): Figure 6.50 Sample attributes for GeneHunter open source software export Affection Status: Additional information about the disease status, including: Disease Freq of B The disease frequency.
Page 249 Chapter 6 | Working with Mapping Data 2. Click the >> button associated with the export attribute. The template attribute name appears in the export attribute box. Click the << button associated with the export attribute to remove the template attribute name. Select samples to export.
Page 250 Affymetrix GeneChip ® Genotyping Analysis Software User’s Guide - Hardy-Weinberg probability value - Mendelian Error rate - SNP Call Rate Before using the Mendelian Error filter, you must: • Assign a sample template with pedigree attributes to the samples. • Import sample attribute data. Click the SNP Filter Conditions button.
Page 251 Chapter 6 | Working with Mapping Data pValue Threshold Specify pValue threshold for filtering SNPs. SNP Call Rate Specify the call rate for filtering SNPs. Mendelian Error Select to filter SNPs with Mendelian inheritance errors (requires use of template attributes and pedigree information for filtered samples) Num Errors per Specify number of errors for filtering SNPs.
Page 252 Affymetrix GeneChip ® Genotyping Analysis Software User’s Guide DataType File Directory path and name for the DataType file. GeneticMapFile Directory path and name for the GeneticMap file. (Merlin format only) Pedigree File Directory path and name for the Pedigree file. Separate file for Select to write genotype information into separate files for each Chromosome...
Page 253 Chapter 6 | Working with Mapping Data 1. Use the dialog box toolbar to locate the directory and enter the file name. 2. Click Save. The path and data file name appear in the textbox. (Merlin format only) Enter the path and file name in the Chromosome Map textbox;...
Page 254 Affymetrix GeneChip ® Genotyping Analysis Software User’s Guide SNP STATISTICS REPORT During export the SNP Statistics Report (Figure 6.56) is generated as a tab-delimited text file. The data can be viewed in Microsoft Notepad, Microsoft Excel, and other text editing and spreadsheet software.
Page 255: Loss Of Heterozygosity Analysis
Chapter 6 | Working with Mapping Data Loss of Heterozygosity Analysis Loss of heterozygosity (LOH) studies compares the allele calls of the SNPs in two different samples. The LOH feature in the Mapping window allows you to survey all of the SNPs in two selected samples for LOH.
Page 256 Affymetrix GeneChip ® Genotyping Analysis Software User’s Guide Figure 6.57 LOH dialog box Select the Reference Analysis from the drop-down list. The drop-down lists only show the analysis results displayed in the Mapping window. Select the Comparison Analysis from the drop-down list. Click Run.
Page 257 Chapter 6 | Working with Mapping Data Figure 6.58 LOH column You can use the copy, sort, export, and other functions of the SNP table with the data in the LOH column(s).
Page 258 Affymetrix GeneChip ® Genotyping Analysis Software User’s Guide...
Page 259 Universal Tag Window Chapter...
Page 260 Chapter...
Page 261: Universal Tag Window
Universal Tag Window The Universal Tag window (Figure 7.1) displays the background- subtracted cell intensities and background values for each probe on selected Universal Tag assays. Figure 7.1 Universal Tag Array window, Tag table The Universal Tag window functions are described in: •...
Page 262: Overview
Affymetrix GeneChip ® Genotyping Analysis Software User’s Guide Overview Each Tag is represented by four features arranged vertically on the GeneFlex ® Tag Array. The Tag-probe designed to be the perfect complement to the tag is called the PM or perfect match probe in the ®...
Page 263 Chapter 7 | Universal Tag Window UNIVERSAL TAG WINDOW TOOLBAR The tool bar (Figure 7.2) provides quick access to some of the commonly used functions of the Universal Tag window. Figure 7.2 Universal Tag window toolbar You can display toolbars with text labels. To display the toolbar button labels, select View Toolbar Text Labels from the menu...
Page 264: Tag Table
Affymetrix GeneChip ® Genotyping Analysis Software User’s Guide Tag Table Each row in the Tag Table displays the following information: Tag ID The reference fragment name. Tag Sequence The sequence position of the reference base in the reference fragment. Sample ID With results: The background-subtracted intensity for the perfect match probe that is a unique 20-mer oligonucleotide designed to be...
Page 265 Chapter 7 | Universal Tag Window toolbar Figure 7.3 Export As dialog box The dialog box toolbar provides standard options for selecting directories and displaying the list of files. Enter a name for the text file in the File name box, then click Save.
Page 266 Affymetrix GeneChip ® Genotyping Analysis Software User’s Guide REMOVING DATA To remove experiments from the Universal Tag window data table (equivalent to closing the analysis results file), do one of the following: • Right-click the Tag table, then select Remove Experiments and the experiment name from the shortcut menu.
Page 267 Chapter 7 | Universal Tag Window Figure 7.5 Find dialog box Enter the desired text for the search (up to 256 alphanumeric characters) in the Find What box. Choose the Match Entire Cell Text option to find an exact match for the search string in a cell.
Page 268 Affymetrix GeneChip ® Genotyping Analysis Software User’s Guide Figure 7.6 Print dialog box The Print dialog box includes the standard MicroSoft Windows print options (select printer, change properties, number of copies, etc., depending upon your system and printer). Select the All or Selection radio button: - All prints out the entire contents of the table.
Page 269 Probe Intensity Window Chapter...
Page 270 Chapter...
Page 271: Probe Intensity Window
Probe Intensity Window The Probe Intensity window displays cell intensity data for Mapping arrays. You can use the Probe Intensity Window to evaluate the cell intensity data for probe cells used to call a particular feature. This chapter provides an overview of the window and describes the window’s: •...
Page 272 Affymetrix GeneChip ® Genotyping Analysis Software User’s Guide • Probe Intensity Table (see page 271): Displays a list of the probe sets with intensity information for each of the samples. Select a probe set in the Table to display in the Intensity Plot. For mapping assays, the Probe Intensity Window displays intensity information for the probe cells used to call the genotype of a particular SNP (see...
Page 273 Chapter 8 | Probe Intensity Window Figure 8.2 Add Cell Intensity Data dialog box Select the cell intensity data for the sample that you want to view and click OK. You can select cell intensity data for up to ten samples at a time. If you wish to display data for additional samples, you will have to select them in separate operations.
Page 274 Affymetrix GeneChip ® Genotyping Analysis Software User’s Guide The Add Cell Intensity Data dialog box provides several options for displaying files (see page 265). Select the cell intensity data for the sample that you want to view and click OK. You can select cell intensity data for only one sample at a time in the dialog box.
Page 275 Chapter 8 | Probe Intensity Window PROBE INTENSITY WINDOW TOOLBAR The tool bar (Figure 8.3) provides quick access to some of the commonly used functions of the Probe Intensity window. Figure 8.3 Probe Intensity window toolbar You can display toolbars with text labels. To display the toolbar button labels, select View Toolbar Text Labels from the menu...
Page 276: Intensity Plot
Affymetrix GeneChip ® Genotyping Analysis Software User’s Guide Intensity Plot The Intensity Plot displays the intensity information for the probe cells of the selected feature as a graph. To select a probe set to display in the Intensity Plot: Click anywhere in the probe set’s row in the Probe Intensity table. Right click in the row to show menu and select Options (or View Options, or click ).
Page 277 Chapter 8 | Probe Intensity Window Click OK. The desired display opens in the Probe Intensity window. BAR AND LINE GRAPH Graphs Color Code Figure 8.5 Intensity Plot for GTYPE assay, bar graph format For Mapping assays (Figure 8.5), the plot displays the intensity values for the probe cells used for the selected SNP (see page 272).
Page 278 Affymetrix GeneChip ® Genotyping Analysis Software User’s Guide Color Code Graphs Figure 8.6 Intensity Plot for GTYPE assay, line graph format The left side of the graph plot displays the graphs of intensity data for the selected feature. The intensity values for each sample are represented by lines or bars of different colors.
Page 279: Probe Intensity Table
Chapter 8 | Probe Intensity Window probe match type (PA, PB, MA, and MB) is drawn with a different color. The probe intensity for forward strand and reverse strand probe quartets are drawn in adjacent charts. Figure 8.7 Trace Plot for GTYPE assay Probe Intensity Table The Probe Intensity table displays a list of the probe sets used in the selected arrays.
Page 280: Data Displayed For Mapping Arrays
Affymetrix GeneChip ® Genotyping Analysis Software User’s Guide Data Displayed for Mapping Arrays Probe Set ID Sample Probe Cell Figure 8.8 Probe Intensity Table for Mapping array For Mapping arrays, the Probe Intensity Table displays a list of the SNPs on the arrays, with the following information presented for each SNP and sample (Figure 8.8):...
Page 281 Chapter 8 | Probe Intensity Window Since a sample can have several pairs of probe quartets, and the table can display more than one sample, you will need to use the scroll bars to view all the data in the table. To learn more about the arrangement of probe cells on Mapping arrays see The GeneChip®...
Page 282 Affymetrix GeneChip ® Genotyping Analysis Software User’s Guide EXPORTING CELL INTENSITY DATA You can export data from the feature table for further analysis in other applications by: • Exporting data as a tabular format file (see page 160) • Copying selected cells to the system Clipboard (see page 302)
Page 283 NetAffx Annotations ™ Chapter...
Page 284 Chapter...
Page 285: Netaffx Annotations
NetAffx Annotations ™ ™ The NetAffx Analysis Center enables researchers to correlate their ® GeneChip array results with array design and annotation information. This resource provides you with unprecedented access to array content information, including probe sequences, gene annotations, and extensive annotation for each SNP. This annotation combines data from multiple sources within the public domain and consolidates it into a single database, providing a level of standardization that facilitates collaboration and sharing of...
Page 286 Affymetrix GeneChip ® Genotyping Analysis Software User’s Guide • The SNP Consortium (TSC) IDs • DBSNP database IDs • Chromosome position of the SNP • Genetic map position of the SNP • Flanking microsatellite markers • Nearest genes ™ You should download updates frequently from the NetAffx site to ensure that you have the most up-to-date information.
Page 287: Downloading Netaffx Annotations
™ Chapter 9 | NetAffx Annotations The default annotations will be displayed after downloading in the Mapping Analysis window. You can also: • Download additional NetAffx annotations (see page 279) • Select particular NetAffx annotations to display (see page 284) •...
Page 288 Affymetrix GeneChip ® Genotyping Analysis Software User’s Guide Figure 9.2 ™ NetAffx Annotation Display dialog box The dialog box displays a list of the available annotations and their download status, checked against the NetAffx server: Category/Display Lists the annotations available. Selection Description A brief description of the annotation.
Page 289 ™ Chapter 9 | NetAffx Annotations If you selected the Preview Latest Annotations List on Network checkbox, the Preview List is updated. Deselect the Preview List checkbox to display the Select Annotations list. The Select Annotations list is displayed automatically if you have not selected the Preview List checkbox.
Page 290 Affymetrix GeneChip ® Genotyping Analysis Software User’s Guide Figure 9.3 ™ NetAffx Annotation Download dialog box The NetAffx Annotations Download displays a list of the annotations available, with three columns of data: Category/ Lists the GeneChip probe array types with annotations available. Download Click the +/- button to display or conceal the available annotations Selection...
Page 291 ™ Chapter 9 | NetAffx Annotations Description A brief description of the annotation. Double-click in the description to view more information about the NetAffx annotation in a browser window. Up to Date? Displays status of annotation files: Yes: the annotation file is stored locally on your computer. No: the annotation file is not stored locally.
Page 292: Selecting Annotations For Display
Affymetrix GeneChip ® Genotyping Analysis Software User’s Guide Click Stop to interrupt the download, and click Download again to restart an interrupted download. The Available Annotations list is updated when the download is complete. Click OK on the NetAffx Annotations Download dialog box to close the dialog box.
Page 293: Setting The Advanced Options
™ Chapter 9 | NetAffx Annotations Click the boxes next to the annotations you wish to display in the Category/Display Selection column. Click OK. The selected annotation is displayed in the SNP Table of the mapping analysis window (Figure 9.6). Figure 9.6 DM SNP Table with NetAffx™...
Page 294 Affymetrix GeneChip ® Genotyping Analysis Software User’s Guide Figure 9.7 ™ Mapping Analysis Options dialog box, NetAffx User Name An identifier for your NetAffx account. Password A password selected for your account. The user name and password are not required for most annotations and will be empty.
Page 295 ™ Chapter 9 | NetAffx Annotations Figure 9.8 Advanced Options dialog box The Advanced Options dialog box allows you to change the URLs ™ and directory for the NetAffx web site: Annotations Local Directory on the client where the annotation information is ™...
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Page 297 Reports Chapter...
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Page 299: Reports
Reports GTYPE generates reports for mapping analyses. These reports include a variety of information about the analyses, including: • A list of the samples analyzed • A summary of information about the allele calls • Quality control information Figure 10.1 Dynamic Model –...
Page 300: Overview
Affymetrix GeneChip ® Genotyping Analysis Software User’s Guide Overview A report is a tab-delimited text file containing statistics and metrics for a group of analysis results. There are two types of reports for mapping analyses: • Algorithm reports are automatically generated when you perform a Mapping analysis.
Page 301 Chapter 10 | Reports Figure 10.2 Open dialog box In the Files of type drop-down list, choose Reports (*.rpt or *.brlmm.rpt). Double-click the report you want to view, or select multiple reports and click Open. The report is displayed in the Report window. If multiple reports are open, click the Report button in the shortcut bar to view the next report.
Page 302 Affymetrix GeneChip ® Genotyping Analysis Software User’s Guide Right-click the selection and choose Report from the shortcut menu. The Select Report Name dialog box opens (Figure 10.3). The default report name is the name of the first analysis results file in the selection.
Page 303 Chapter 10 | Reports Figure 10.4 Report dialog box Select the analysis results files for the report and click OK. The Select Report Name dialog box opens (Figure 10.3). The default report name is the name of the first analysis results file in the selection.
Page 304 Affymetrix GeneChip ® Genotyping Analysis Software User’s Guide MAPPING REPORTS The Mapping Algorithm report and the Mapping Analysis Results report contain the same components. Figure 10.5 Dynamic Model Mapping algorithm report...
Page 305 Chapter 10 | Reports Figure 10.6 BRLMM mapping algorithm (mapping array) report Mapping Algorithm Report The Mapping algorithm report contains basic information about the SNP calls and the QC probe performance for the analyzed samples Figure 10.5 Figure 10.6. Mapping Analysis Results Report The Mapping Analysis Results report compiles the report information for user-selected analysis results files.
Page 306 Affymetrix GeneChip ® Genotyping Analysis Software User’s Guide Mapping Report Components The table below lists the report components. Table 10.1 Mapping report components (MPAM mapping and Dynamic Model mapping analyses) Report Component Description Number of SNPs on array. Total number of SNPs Number of QC SNPs on array.
Page 307: Working With Reports
Chapter 10 | Reports Table 10.1 Mapping report components (MPAM mapping and Dynamic Model mapping analyses) Report Component Description MPAM Call Rate: The number of SNPs called with MPAM algorithm/Total MCR (DM mapping only) number of SNPs checked with the MPAM algorithm for QC purposes (see Contamination QC Check, on page 345).
Page 308 Affymetrix GeneChip ® Genotyping Analysis Software User’s Guide You can display toolbars with text labels. To display the toolbar button labels, select View Toolbar Text Labels from the menu bar. Table 10.2 Report toolbar button functions Menu Bar Command Toolbar Function Button Edit...
Page 309 Chapter 10 | Reports Figure 10.8 Font dialog box The Font dialog box allows you to select different fonts, styles and sizes for displaying the report. Select the desired options for the font. Click OK. The report is displayed with the selected font options. SEARCHING A REPORT To start a text search: Click the Find button...
Page 310 Affymetrix GeneChip ® Genotyping Analysis Software User’s Guide Figure 10.9 Find dialog box Enter the text string for the search (up to 256 alphanumeric characters). Choose the Match case or Direction option, and click Find Next. command finds all strings that match the text string for the Find search.
Page 311 Chapter 10 | Reports PRINTING A REPORT To print all or part of a report. Open the report that you want to print. If more than one report is open, click the Report shortcut button to view the different reports. Click the Print button ;...
Page 312 Affymetrix GeneChip ® Genotyping Analysis Software User’s Guide...
Page 313 Installing GTYPE Software Appendix...
Page 314 Appendix...
Page 315: Appendix A Installing Gtype Software
Installing GTYPE Software This appendix provides detailed instructions for installing the ® GeneChip Mapping Analysis Software (GTYPE). It also includes instructions for installing the GTYPE server component in GCOS Server. It includes the following sections: • Overview (see below) • Requirements (see page 307) •...
Page 316: Installation
Affymetrix GeneChip ® Genotyping Analysis Software User’s Guide The screen captures depicted in this manual may not exactly match the windows displayed on your screen. It is recommended that there is at least 500 MB of available disk space for the installation. Installation To install the GTYPE software: ®...
Page 317 Appendix A | Installing GTYPE Software Figure A.2 GTYPE software install Welcome window Click Next. The Affymetrix, Inc. End User License Agreement opens (Figure A.3). Figure A.3 GTYPE software License Agreement window Review the contents and click Yes in each window to accept the terms of the licensing agreement.
Page 318 Affymetrix GeneChip ® Genotyping Analysis Software User’s Guide If the No option is selected, the installation program will exit and GTYPE software will not be installed. After you accept the End User License Agreement, the Customer Information window opens (Figure A.4).
Page 319 Appendix A | Installing GTYPE Software Figure A.5 GTYPE Choose Destination Location window Select the destination where GTYPE software will be installed. C:\Program Files\Affymetrix\GTYPE 4.1 is the default location. Click Next. The Ready to Install the Program window opens (Figure A.6).
Page 320 Affymetrix GeneChip ® Genotyping Analysis Software User’s Guide The installation begins. The Setup Status window opens (Figure A.7). Figure A.7 GTYPE software Setup Status window After the files are copied, the InstallShield Wizard Complete window opens (Figure A.8). Figure A.8 GTYPE software Install Complete window To exit the InstallShield Wizard, click Finish.
Page 321: Selecting A Database
Appendix A | Installing GTYPE Software Selecting a Database You may use GTYPE software with GCOS Server, as well as with a standalone process database. To switch from a local to a remote GCOS Server database: Select Tools Defaults from the menu bar. The Defaults dialog box opens.
Page 322: Installing Gtype Server Components In Gcos Server
Affymetrix GeneChip ® Genotyping Analysis Software User’s Guide Installing GTYPE Server Components in GCOS Server The GTYPE server components must be installed on the GCOS Server before the server can be used with the GTYPE software v.4.1 client. This information is provided for the use of system administrators. To install the GTYPE Server components: ®...
Page 323 Appendix A | Installing GTYPE Software Figure A.11 GTYPE software Install Welcome window Click Install. Status windows displays the progress of the installation. After the files are copied, the InstallShield Wizard Complete window opens (Figure A.12). Figure A.12 GTYPE software InstallShield Wizard Complete window To exit the InstallShield Wizard and restart your computer, click Finish.
Page 324 Affymetrix GeneChip ® Genotyping Analysis Software User’s Guide...
Page 325 MPAM Mapping Algorithm Appendix...
Page 326 Appendix...
Page 327: Mpam Mapping Algorithm
MPAM Mapping Algorithm The MPAM (Modified Partitioning Around Medoids) mapping algorithm analyzes the cell intensity data from the Affymetrix ® GeneChip Mapping 10K Array, to determine the alleles of the SNPs represented in the sample. This appendix describes: • The GeneChip 10K mapping array (see below) •...
Page 328 Affymetrix GeneChip ® Genotyping Analysis Software User’s Guide ...C CGG TGAT TAT G AC CTAC TAT AA.. . Reference Sequence TG GATG ATA TT G GCC ACTA ATA C Probe Pair Allele A G GCC ACTA ATA C TG GATG ATA TT Probe Quartet G GCC ACTA ATA C TG GATG ATA TT...
Page 329: The Mpam Algorithm
Appendix B | MPAM Mapping Algorithm SNP site Reference .. .T A GG G GG TG A TT AT G AA C CT AC T AT TT A GG A .. . Sequence offset CC C CA C TA AT A CT TG G AT G AT AA A T Probe CCCCC ACTA ATAC T T GG A TG AT A AA Sequences...
Page 330 Affymetrix GeneChip ® Genotyping Analysis Software User’s Guide Calculate the call zone scores, also known as the Distance to Radius ratio (DTR), for each allele type of the SNP using the model, and evaluate the call zone score to make an allele call for the SNP (see page 325).
Page 331 Appendix B | MPAM Mapping Algorithm Evaluating Discrimination Scores Having calculated the individual discrimination scores for the probe pairs, the algorithm evaluates these scores to determine if the SNP passes the detection filter: The median discrimination scores are calculated for the forward and reverse strands for the A and B alleles: DS(s,A) = median of the allele A sense strand probe pair discrimination scores...
Page 332 Affymetrix GeneChip ® Genotyping Analysis Software User’s Guide CALCULATING MEDIAN RELATIVE ALLELE SIGNALS (RAS) The relative allele signal is a measure of the intensities of the perfect match cells for the A and B alleles of a SNP. The algorithm calculates median relative allele signal scores (RAS) for the sense and antisense strands of the SNP, using the intensity values for the probe cells: The RAS value for each probe quartet is calculated using the...
Page 333 Appendix B | MPAM Mapping Algorithm median of the RAS values for the antisense direction probe quartets and uses this value as the RAS value for the antisense direction. Normally the RAS values are between 0-1. If the probe set for the SNP does not pass the discrimination filter, the RAS value is not calculated, but set to -2, and the call zone score, also known as the distance to radius (DTR) ratio, is set to 10.
Page 334 Affymetrix GeneChip ® Genotyping Analysis Software User’s Guide Sense and Antisense plots for samples Model Medoids RAS2 Antisense RAS1 Sense Figure B.3 Typical distribution of RAS values from different samples for a SNP For each SNP, the sense and antisense RAS values from all the samples were evaluated to find those falling into three distinct clusters corresponding to the AA, AB, and BB allele calls (Figure...
Page 335 Appendix B | MPAM Mapping Algorithm For each possible allele call: The sense and antisense RAS values for a given SNP are plotted against that SNP’s three model medoids (Figure B.4). Model Medoids Sample RAS value RAS2 Antisense Call Zone Score for AA medoid = D/R RAS1 Sense Figure B.4 Calculating the call zone score (DTR value)
Page 336 Affymetrix GeneChip ® Genotyping Analysis Software User’s Guide Calling the Allele The algorithm compares the sample’s call zone scores for the three possible allele calls to the algorithm’s call zone bound, also known as the call zone radius. • If the sample’s call zone score for a particular allele is lower than the call zone bound, the SNP is assigned that allele call, and that call zone score is displayed in the SNP table of the MPAM mapping analysis window.
Page 337 Appendix B | MPAM Mapping Algorithm Sense and Antisense plots for samples Model Medoids RAS2 Antisense RAS1 Sense Figure B.5 Typical distribution of RAS values for an X chromosome SNP for samples from males Sense and Antisense plots for samples Model Medoids RAS2 Antisense...
Page 338 Affymetrix GeneChip ® Genotyping Analysis Software User’s Guide The gender may be specified for the sample when the experiment is first set up (see Using the Gender Attribute Values, on page 130). If the gender is not specified, the algorithm determines the gender of the sample using the following process: The alleles for the SNPs on the X chromosome are first called using a generic model.
Page 339: Mpam Mapping Algorithm Settings
Appendix B | MPAM Mapping Algorithm The HCR bound can be adjusted using the HCRBound parameter. For more information, see MPAM Mapping Algorithm Settings REFERENCES Refer to the appropriate tech note for more information about the MPAM mapping algorithm. MPAM Mapping Algorithm Settings The MPAM mapping algorithm incorporates user modifiable settings which influence call rate and call accuracy.
Page 340 Affymetrix GeneChip ® Genotyping Analysis Software User’s Guide Select array type Enter a new value for the selected item here Figure B.7 Mapping Algorithm Settings dialog box, MPAM settings displayed Select the array type you are analyzing from the Probe Array Type drop-down box.
Page 341 Appendix B | MPAM Mapping Algorithm Table B.1 MPAM mapping algorithm, user-adjustable parameters Item Description Effect of Changing the Settings Setting Number Change of Calls HCRBound Heterozygote Call Ratio limit for gender determination algorithm. Determining Sample Gender, on page 328. CallZoneBound Call Zone limit for DTR ratio value.
Page 342 Affymetrix GeneChip ® Genotyping Analysis Software User’s Guide...
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Page 344 Appendix...
Page 345: Appendix C Dynamic Model Mapping Algorithm
Dynamic Model Mapping Algorithm The Dynamic Model mapping algorithm analyzes the cell intensity ® data from an Affymetrix GeneChip Human Mapping 100K or 500K array set to determine the alleles of the SNPs represented in the sample. This appendix describes: •...
Page 346 Affymetrix GeneChip ® Genotyping Analysis Software User’s Guide ...C CGG TGAT TAT G AC CTAC TAT AA.. . Reference Sequence TG GATG ATA TT G GCC ACTA ATA C Probe Pair Allele A G GCC ACTA ATA C TG GATG ATA TT Probe Quartet G GCC ACTA ATA C TG GATG ATA TT...
Page 347: The Dynamic Model Mapping Algorithm
Appendix C | Dynamic Model Mapping Algorithm SNP site Reference .. .T A GG G GG TG A TT AT G AA C CT AC T AT TT A GG A .. . Sequence offset CC C CA C TA AT A CT TG G AT G AT AA A T Probe CCCCC ACTA ATAC T T GG A TG AT A AA Sequences...
Page 348 Affymetrix GeneChip ® Genotyping Analysis Software User’s Guide • Null: Intensities for both PM and MM are all background intensities. • AA: The PM cell intensity for the A allele is high and the other three cells are background. • AB: The PM cell intensities for the A and B alleles are high and the MM cell intensities are background.
Page 349 Appendix C | Dynamic Model Mapping Algorithm The resulting output includes: - Genotype call - Confidence score (rank score for genotype call used) - Rank scores for all genotype calls In a separate step, the software runs MPAM analysis on a selected set of SNPs on the Dynamic Model chips for contamination QC check (see...
Page 350 Affymetrix GeneChip ® Genotyping Analysis Software User’s Guide with respect to all parameters and solving the corresponding system of equations. As an example, for model AA, the perfect match for AA is assumed as foreground, all the other three are assumed as background and evenly distributed, hence we have: ⎛...
Page 351 Appendix C | Dynamic Model Mapping Algorithm Figure C.4 S-value matrix GENOTYPE CALLS USING WILCOXON SIGNED-RANK TEST Next, the confidence of each model is calculated using a rank score. The rank score is a type of probability where the smaller the rank score, the larger the probability the model is correct.
Page 352 Affymetrix GeneChip ® Genotyping Analysis Software User’s Guide Most significant rank score among these will determine the call for the SNP Figure C.5 Calculating rank scores The model with the most significant rank score (smallest value) is considered as the candidate model. The rank score is compared to a user adjustable threshold;...
Page 353 Appendix C | Dynamic Model Mapping Algorithm Notice that even with RS < threshold the genotype call still could be no call since the Null model may be the most likely model. For more information, see One-sided Wilcoxon’s Signed Rank Test, on page 347.
Page 354 Affymetrix GeneChip ® Genotyping Analysis Software User’s Guide performance and the ability to be a sensitive detector of sample contamination across large data sets. Using this subset also allows the software to quickly derive contamination metrics without the additional computational burden of having to make an extra set of calls on the entire array.
Page 355 Appendix C | Dynamic Model Mapping Algorithm GENDER CALLS A gender call is made for the sample by comparing the heterozygous call ratio for X chromosome SNPs to a threshold value set in the software (see Determining Sample Gender, on page 328).
Page 356 Affymetrix GeneChip ® Genotyping Analysis Software User’s Guide Table C.1 Absolute values Original non-zero convert to position differences absolute values d1 = 2 a1 = 2 d2 = 1 a2 = 1 d3 = -2 a3 = 2 d4 = 0.5 a4 = 0.5 d5 = 0.5 a5 = 0.5...
Page 357 Appendix C | Dynamic Model Mapping Algorithm Then we form the sum of positive signed ranks, S = sum(u(s , i = 1:n), where u(s )=1 if s > 0, and u(s ) = 0 if s < 0. In our example, S = s = 10.5.
Page 358 Affymetrix GeneChip ® Genotyping Analysis Software User’s Guide Table C.3 Random Signed Ranks for rank score evaluation -1.5 -1.5 -4.5 -4.5 -1.5 -4.5 -4.5 -1.5 -4.5 -4.5 -1.5 -1.5 -4.5 -4.5 -1.5 -1.5 -4.5 -1.5 -1.5 -4.5 -4.5 -4.5 -1.5 -4.5 -4.5 -1.5...
Page 359: Dynamic Model Mapping Algorithm Settings
Appendix C | Dynamic Model Mapping Algorithm All signed ranks above 10.5 (a total of 5) are given a weight of 1 and signed ranks equal to 10.5 (a total of 4) are given a weight of 0.5. In our example: 1 ∗...
Page 360 Affymetrix GeneChip ® Genotyping Analysis Software User’s Guide Select the array type you are analyzing from the Probe Array Type drop-down box. The parameters for that array type are displayed. To change a setting: Click the item you want to change. The current value for the item is displayed (Figure C.6).
Page 361 Bayesian Robust Linear Model with Appendix Mahalanobis (BRLMM) Distance Classifier Algorithm...
Page 362 Appendix...
Page 363: Bayesian Robust Linear Model With Mahalanobis (Brlmm) Distance Classifier Algorithm
Bayesian Robust Linear Model with Mahalanobis (BRLMM) Distance Classifier Algorithm The BRLMM (Bayesian Robust Linear Model with Mahalanobis) distance classifier algorithm is an extension of Nusrat Rabbee and Terry Speed’s RLMM (Robust Linear Model with Mahalanobis) distance classifier algorithm [1]. BRLMM provides a significant improvement over the DM (Dynamic Model) algorithm in two important areas.
Page 364: Introduction
Affymetrix GeneChip ® Genotyping Analysis Software User’s Guide Introduction Highly accurate and reliable genotype calling is an essential component of any high-throughput SNP genotyping technology. The Dynamic Model (DM) algorithm [2], which has been extensively used ® with the Affymetrix GeneChip Human Mapping 100K Array Set and ®...
Page 365 Appendix D | Bayesian Robust Linear Model with Mahalanobis (BRLMM) Distance Classifier Al- probe intensities than does DM, making them far more robust in the presence of real world data. Figure D.1 below presents an overview of the BRLMM workflow. Figure D.1 BRLMM Algorithm Workflow...
Page 366 Affymetrix GeneChip ® Genotyping Analysis Software User’s Guide The first step in the workflow is to normalize the probe intensities and calculate allele signal estimates for each SNP in each experiment. The allele signal estimates are then transformed to a two-dimensional space in which the underlying genotype clusters are well behaved in terms of having similar variances for each of the clusters.
Page 367: Normalization And Allele Summarization
Appendix D | Bayesian Robust Linear Model with Mahalanobis (BRLMM) Distance Classifier Al- Normalization and Allele Summarization The normalization and allele summarization portion of the BRLMM algorithm consists of producing a summary value for each allele of a SNP in each experiment. The A allele summary value increases and decreases with the quantity of the A allele in the target genome.
Page 368: Clustering Space Transformation
Affymetrix GeneChip ® Genotyping Analysis Software User’s Guide constrained to sum to zero. We repeat this step by fitting the above model separately to the allele B probes. For each SNP n, the multi-chip model reduces and produces 2-dimensional estimates of S ), which are summary measures of the allele A and B intensities for chip i.
Page 369 Appendix D | Bayesian Robust Linear Model with Mahalanobis (BRLMM) Distance Classifier Al- The cluster centers, estimated using DM, are determined. Each plotted point corresponds to an estimate of the cluster center for one genotype in one SNP, with color indicating genotype (AA = red, AB = blue, BB = green).
Page 370: Calling Genotypes
Affymetrix GeneChip ® Genotyping Analysis Software User’s Guide enable appropriate balancing of heterozygous and homozygous performance – larger values of K make het calls more likely and conversely, smaller values of K decrease the tendency towards het calls. Calling Genotypes We call genotypes by a template-matching procedure comparing the transformed allele signal values observed in an experiment to the typical values (prototype) we expect for each genotype.
Page 371: Estimating Cluster Centers And Variances
Appendix D | Bayesian Robust Linear Model with Mahalanobis (BRLMM) Distance Classifier Al- σ σ symmetric with . The distance d is computed as defined above. The confidence we assign to this call is d , where d is the smallest distance of the three and d is the second smallest distance.
Page 372 Affymetrix GeneChip ® Genotyping Analysis Software User’s Guide Figure D.4 Examples of SNP clustering The samples and SNPs in Figure D.4 are part of HapMap, and therefore allow an independent estimate of the genotype for each case, indicated by the color of each point (AA = red, AB = blue, BB = green).
Page 373 Appendix D | Bayesian Robust Linear Model with Mahalanobis (BRLMM) Distance Classifier Al- in the case of the SNP on the left, which is quite shifted from the ideal heterozygotes contrast value of zero. To start the process, you must seed with some initial genotype estimates from which to build the generic prior.
Page 374 Affymetrix GeneChip ® Genotyping Analysis Software User’s Guide W = The 6x6 block-diagonal variance-covariance matrix of within-genotype variances and covariances. The entries of the matrix are w with w = 0 for |i-j| > 1. Some or all of these entries may be null, if there are not at least two DM initial estimates of one or more of the three genotypes.
Page 375: Special Cases
Appendix D | Bayesian Robust Linear Model with Mahalanobis (BRLMM) Distance Classifier Al- Again, this has the intuitively sensible property that when there is little or no labeled data available, the estimate of cluster centers will be driven mainly by the prior estimate m. When there is alot of data available for a given genotype, the estimate will be driven by v.
Page 376 Affymetrix GeneChip ® Genotyping Analysis Software User’s Guide XX individuals are handled using the standard BRLMM methodology for all chrX SNPs; that is, three cluster centers are extracted from the data along with covariance matrices and are used to classify observations.
Page 377: Results
Appendix D | Bayesian Robust Linear Model with Mahalanobis (BRLMM) Distance Classifier Al- Results The results in Table D.1 are based on combining the Nsp and Sty chips. The default BRLMM threshold is set to 0.5, and it can be tuned for higher call rates or higher accuracy depending on which one is more suitable for the requirements of downstream analysis.
Page 378: Discussion
Affymetrix GeneChip ® Genotyping Analysis Software User’s Guide Table D.1 Performance on HapMap dataset for DM and BRLMM at various fixed thresholds. Method Confidence Overall Overall Threshold Call Rate Call Call Concordance Concordance Concordance Rate Rate 0.26 94.16% 97.24% 86.32% 99.15% 99.39% 98.38%...
Page 379: Brlmm Mapping Algorithm Settings
Appendix D | Bayesian Robust Linear Model with Mahalanobis (BRLMM) Distance Classifier Al- minimum number of samples required is six. However, performing a run with only six samples is not advised. Another consideration is the extent to which data sets can be combined.
Page 380 Affymetrix GeneChip ® Genotyping Analysis Software User’s Guide Select array type Enter a new value for the selected items Figure D.5 Mapping Algorithm Settings dialog box, Dynamic Model mapping settings deposed Select the array type you are analyzing from the Probe Array Type drop-down box.
Page 381: Brlmm Ram Requirements
Appendix D | Bayesian Robust Linear Model with Mahalanobis (BRLMM) Distance Classifier Al- Table D.2 BRLMM parameter settings Parameter Default Value Description Score Threshold Maximum score (i.e. lowest confidence) at which to make a call, all calls of lower confidence get no call. BlockSize How many probe sets to process at one time;...
Page 382 Affymetrix GeneChip ® Genotyping Analysis Software User’s Guide A more specific problem that may be encountered on a multi-user or multi-processor system is running out of memory when a BRLMM run is initiated and another large-memory BRLMM run is initiated soon afterwards.
Page 383: References
Appendix D | Bayesian Robust Linear Model with Mahalanobis (BRLMM) Distance Classifier Al- On most 32 bit systems (i.e. Intel Pentium, Intel Xeon, Microsoft Windows), you cannot use more than ~2 gigabytes of RAM with a single process, even if there is more available. References 1.
Page 384 Affymetrix GeneChip ® Genotyping Analysis Software User’s Guide...
Page 385 Mapping Tool Algorithms Appendix...
Page 386 Appendix...
Page 387: Sample Mismatch Algorithm
Mapping Tool Algorithms Algorithms/formulas for the different mapping tools: • Sample Mismatch Algorithm (see below) • Filter Algorithms (see page 380) Sample Mismatch Algorithm The Sample Mismatch report uses the Mismatch score to determine if two samples are the same. The Mismatch score for a single SNP is the number of alleles shared between two individuals, either 0, 1, or 2.
Page 388: Filter Algorithms
Affymetrix GeneChip ® Genotyping Analysis Software User’s Guide • Sib pairs and parent-offspring pairs should have Mismatch scores between 1.3-1.8 • Unrelated pairs should have Mismatch scores between .9 - 1.3. The Mismatch chip variance can be used to resolve Sib and parent- offspring relations.
Page 389 Appendix E | Mapping Tool Algorithms ALLELE FREQUENCY The allele frequency for the A allele is calculated as Number of AA calls + 0.5 * Number of AB Calls -------------------------------------------------------------------------------------------------------------- - Total Number of Calls where the Total Number Calls does not include the no call samples, i.e.
Page 390 Affymetrix GeneChip ® Genotyping Analysis Software User’s Guide Where: Number of AA calls ---------------------------------------------- - Total Number calls Number of BB calls --------------------------------------------- - Total Number calls Number of AA calls + 0.5 * Number of AB calls ------------------------------------------------------------------------------------------------------------ - Total Number calls Number of BB calls + 0.5 * Number of AB calls ----------------------------------------------------------------------------------------------------------- -...
Page 391 Appendix E | Mapping Tool Algorithms The sample set can consist of one or more families. If the Mendelian errors for any one of the families is above the threshold, the user shall have the option to filter the SNPs by either: •...
Page 392 Affymetrix GeneChip ® Genotyping Analysis Software User’s Guide...
Page 393 IUPAC Base Codes Appendix...
Page 394 Appendix...
Page 395 IUPAC Base Codes Table F.1 IUPAC Base Codes IUPAC Code Group Base(s) Adenine Cytosine Guanine Thymine A or C aMino A or G puRine A or T (U) Weak interaction (2 H bonds) C or T (U) pYrimidine C or G Strong interaction (3 H bonds) G or T(U)
Page 396 Affymetrix GeneChip ® Genotyping Analysis Software User’s Guide...
Page 397 File Types Appendix...
Page 398 Appendix...
Page 399 File Types Probe Information Files The probe information or library files contain information about the probe array design characteristics, probe utilization and content, and scanning and analysis parameters. These files are unique for each probe array type. Experiment Data Files You create the experiment information file (*.exp) during experiment ®...
Page 400 Affymetrix GeneChip ® Genotyping Analysis Software User’s Guide Table G.1 ® Affymetrix file types Experiment Created in... Description Data File Name Report file GTYPE Report files used to provide additional (*.rpt) information about analysis algorithm and results. Graphics file GTYPE A standard file format for graphic images.
Page 401 Working with Windowpanes & Columns Appendix...
Page 402 Appendix...
Page 403 Working with Windowpanes & Columns Resizing Windowpanes You can resize windowpanes. Place the mouse pointer over a windowpane border so that it changes to a double arrow Figure H.1 Resize windowpanes horizontally or vertically (GTYPE) Drag the border to resize the windowpane. Resizing or Hiding Table Columns You can resize or hide columns in the table view.
Page 404 Affymetrix GeneChip ® Genotyping Analysis Software User’s Guide To hide a column, drag the left or right cell border of the column header until the column width is reduced to zero, or right-click the column header in the table and click Hide Column in the shortcut menu.
Page 405 Hot Key Descriptions Appendix...
Page 406 Appendix...
Page 407 Hot Key Descriptions Table I.1 Hot key descriptions Menu Bar Command Hot Key File Open Ctrl + O File Print Ctrl + P Edit Ctrl + X Edit Copy Cells or Ctrl + C Edit Copy Edit Paste Ctrl + V Edit Image Settings Edit...
Page 408 Affymetrix GeneChip ® Genotyping Analysis Software User’s Guide Table I.1 Hot key descriptions Menu Bar Command Hot Key 1, 2, 3, etc. (toggle between open image windows) (Image window zoom in) (Image window zoom out) Shift+O (Image window full zoom out) (intensity autoscale) Help...
Page 409 Index...
Page 411: Index
Index Symbols selecting 60 chip averaged Mismatch score AttributeImporter Tool .cel extension GCOS Server security roles Classic view See also cell intensity data 186, 193 Color dialog box .chp extension attributes See also analysis results file importing 185 (*.chp) in sample templates 182 .dat extension data export selecting in AttributeImport-...
Page 412 Affymetrix GeneChip ® Genotyping Analysis Software User’s Guide conventions used 6 help online 8 report file (*.rpt) 392 heterozygosity DSBound files loss of heterozygosity analy- opening 67 sis 247 DTR ratio 147, 155 viewing information 62 heterozygote call ratio (HCR) Dynamic Model Mapping algo- FileSets 330, 333...
Page 413 Index toolbar 267 probe set intensity data linking to samples NetAffx Analysis Center viewing LOH analysis NetAffx annotations in Image window 92 Advanced Options dialog LOH dialog box in Probe Intensity win- box 286 loss of heterozygosity analysis dow 263 Display dialog box 279, 284 process database 49, 307...
Page 414 Affymetrix GeneChip ® Genotyping Analysis Software User’s Guide resizing windowpanes exporting data from 159 data tree 57 printing 163 main display area 55 overview 54 Sort dialog box status log 55 starting GTYPE sample changing process database assigned in GCOS 60 renaming 69 status log virtual array...

Newport iServer MicroServer iTHX-M Operator's Manual

Introduction

CHAPTER 1 GTYPE Overview

CHAPTER 2 Getting Started

CHAPTER 3 Working with Images

CHAPTER 4 Analyzing Cell Intensity Data

CHAPTER 5 Mapping Analysis Window

CHAPTER 6 Working with Mapping Data

CHAPTER 7 Universal Tag Window

CHAPTER 8 Probe Intensity Window

CHAPTER 9 Netaffx Annotations

CHAPTER 10 Reports

Appendix A Installing GTYPE Software

Appendix B MPAM Mapping Algorithm

MPAM Mapping Algorithm

Appendix C Dynamic Model Mapping Algorithm

Bayesian Robust Linear Model with Mahalanobis (BRLMM) Distance Classifier Algorithm

Appendix D Bayesian Robust Linear Model with

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