Applied Biosystems 7900HT User Manual page 190

Chapter 6 Analyzing Real-Time Data
Analyzing the
Run
6-12 Applied Biosystems 7900HT Fast Real-Time PCR System and SDS Enterprise Database User Guide
September 1, 2004 11:39 am, CH_Real-Time.fm
c. Do one of the following. Select the:
Automatic Baseline option button to have the software calculate a baseline
for the selected detector(s).
Manual Baseline option button, and enter Start and End cycle values to
apply to the selected detector(s).
Manual Baseline option button, and leave the Start and End cycles fields
empty. (You will need to set the values manually as explained on
4. If necessary, repeat
The threshold and baseline values set in
IMPORTANT!
detector specific, and must be set for each individual detector used on in the
plate document.
5. Click to accept the analysis settings and exit.
6. Analyze the data as explained below.
After you have configured the analysis settings, you can analyze the run data. During
the analysis, the software mathematically transforms the raw data to establish a
comparative relationship between the spectral changes in the passive reference dye
and those of the reporter dye. Based on that comparison, the software calculates a
cycle threshold (C ) for each reaction (standard and unknown). The software then
T
generates a standard curve for the run by plotting the standard samples on a graph of
C versus initial copy number.
T
See Appendix D, "Theory of Operation,"
Note:
software mathematical transformation of real-time run data.
1. Click (or select Analysis > Analyze).
The SDS software analyzes the run data and displays the results in the Results
tab.
2. Choose from the following:
• If using the AutoC
the detectors on the plate, verify that the software has called the settings
correctly for each detector as described on
• If you choose to set the baseline and threshold values manually, set them
for each detector on the plate as explained on
3. If you choose to remove outliers manually, visualize and eliminate outliers from
the analyzed run data as explained on
DRAFT
steps 2 through 3 for any additional detectors.
algorithm to set the baseline and threshold values for
T
page
step 3 on page 6-11
for a detailed description of the SDS
page 6-46,
page 6-46.
6-46.
page 6-46.)
are