Applied Biosystems 7900HT Fast Real-Time PCR System and SDS ...

Chapter 5Analyzing End-Point DataAnalyzing an Allelic Discrimination RunUser AccessRequirementAbout theAnalysisConfiguring theAnalysis SettingsThere is no access requirement. All users can analyze allelic discrimination data.The analysis of SNP (or genotyping) data involves the automatic or manual “calling”of sample data for each marker. The “calls” are data labels assigned to individualsamples to reflect their genomic content. The SDS software can call sample data.The SDS software can call sample data:• Manually, using the toolbar and scatterplot.• Automatically, using the “AutoCalling” system (see “About the AutoCallingSystem” on page 5-7).Before analyzing your data, you must configure the analysis settings for each markerthat you want to analyze using the AutoCalling algorithm. The analysis settings arespecific to each marker and must be set for each one individually.IMPORTANT! You need to configure the analysis settings for a marker only if youwant to use the AutoCalling system to analyze it.To configure the analysis settings:1. Click (or select Analysis > Analysis Settings).2. Do one of the following:To set the analysis settings for:• A single marker, select a marker of interest from the Marker drop-down list.• All markers, select All markers from the Marker drop-down list.3. In the Analysis Settings dialog box:a. Select the Auto caller enabled check box to activate the AutoCallingsystem for the associated marker.b. If you expect the analyzed data to consist of only two clusters, select the2-Cluster Calling check box.c. Enter a percentage value in the Quality field to apply as the quality intervalfor AutoCalling samples.4. Repeat steps 2 through 3 for the remaining markers on the plate document.5. When finished, click .Analyzing theDataDuring the analysis, the software employs several algorithms to generate from theraw data a more direct measure of the relationship between the spectral changes inthe samples.To analyze the data:1. Click (or select Analysis > Analyze).The SDS software analyzes the run data and displays the results in the Results tab.5-12 Applied Biosystems 7900HT Fast Real-Time PCR System and SDS Enterprise Database User GuideDRAFTSeptember 1, 2004 11:39 am, CH_End-Point.fm