Applied Biosystems 7900HT User Manual

DRAFT
September 1, 2004 11:39 am, CH_Real-Time.fm
Chapter 6 Analyzing Real-Time Data
6-30 Applied Biosystems 7900HT Fast Real-Time PCR System and SDS Enterprise Database User Guide
8. In the Endogenous Control Detector drop-down list, select the detector
representing the endogenous control for your study.
IMPORTANT! The detector used as the endogenous control must be present in
all sessions attached to the study.
9. Select the option button (Multiplexed or Non-Multiplexed) to indicate the type
of endogenous control used.
Note: The Multiplexed or Non-Multiplexed option buttons are active only if the
sessions loaded for analysis contain both multiplex and non-multiplex reactions.
10. In the RQ Min\Max Confidence drop-down list, select the confidence value
you want the software to use when generating error bars for the gene expression
plot.
11. If desired, select the Export Individual ∆C
T
option button to instruct the SDS
software to display the ∆C
T
values for individual samples belonging to replicate
groups. If the option is not selected, the software displays the average ∆C
T
for
the replicate group.
12. Click to accept the analysis settings and exit.
13. Analyze the data as explained in “Analyzing the Data” on page 6-30.
Analyzing the Study Data
Analyzing
the Data
During the analysis, the software mathematically transforms the raw data to establish
a comparative relationship between the spectra changes in the passive reference dye
and those of the reporter dye. Based on that comparison, the software calculates a
cycle threshold (C
T
) for each reaction (endogenous control and unknown).
Note: See Appendix D, “Theory of Operation,” for a detailed description of the SDS
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 you choose to set the baseline and threshold values manually, set them
for each detector on the plate as explained on page 6-46.
• If using the AutoC
T
algorithm to set the baseline and threshold values for
the detectors on the plate, verify that the software has called the settings
correctly for each detector by following the procedure for manually setting
the baseline and threshold on page 6-46 without adjusting the settings.
3. If you choose to remove outliers manually, visualize and eliminate outliers from
the analyzed run data as explained on page 6-46.

Applied Biosystems 7900HT Specifications

General

Brand	Applied Biosystems
Model	7900HT
Category	Laboratory Equipment
Language	English