Working With Images; Viewing Cell Intensity Images - Newport iServer MicroServer iTHX-M Operator's Manual

Viewing Cell Intensity 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
• View probe cell data (see
• Highlight a probe set or selected probes in the image (see
• Create and view bookmarks in an image (see
• Adjust the defaults settings for the Image window (see
You can also use the Probe Intensity window to view probe cell
intensity data for a selected base or SNP (in mapping assays). For
more information, see
page 263.
The Affymetrix GeneChip
automatically generates the cell intensity data (*.cel) from the scan
image (*.dat file). It computes a single intensity value for each probe
cell (feature) on the probe array and saves it to the cell intensity data
file with a .cel extension.
GTYPE analyzes the cell intensity data and saves the results to an
analysis results file with a .chp extension.
The Image window displays the cell intensity data.
To open one or more cell intensity data files, do one of the
1.
following in the data tree:
- Double-click the cell intensity data file.
- Select the cell intensity data files that you want to open, right-
click the selection, and click Open in the shortcut menu.
- If no analysis results or report file is open, drag the cell
intensity data file(s) to the main display area
page 89)
,
Chapter 8 Probe Intensity Window
®
Operating System (GCOS) application
79
page 84)
page 92)
page 98)
page 101)
, on
(Figure 3.1).