Software, Version 2.1 Owner's manual

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6.7.7 Vertical Threshold ..................................................................................................74
6.7.8 Horizontal Threshold ..............................................................................................74
6.7.9 Normalize Data ......................................................................................................74
6.7.10 Restore Default....................................................................................................75
6.8 End Point Analysis........................................................................................................75
6.8.1 The End Point Analysis Settings ………………………………………………………………………….75
6.8.2 End Point Analysis Spreadsheet ..............................................................................77
6.8.3 Recalculate Button .................................................................................................78
6.9 Gene Expression Analysis. ............................................................................................78
6.9.1 Normalized Gene Expression (ddC
T,
∆∆C
T
) ...............................................................80
6.9.2 Relative Quantity (dC
T,
∆C
T
)....................................................................................81
6.9.3 Specifying Gene and Condition Labels for Gene Expression Analysis..........................82
6.9.4 Setting Analysis Parameters for Gene Expression Analysis Using the Settings Tab......85
6.9.4.1 Gene List: Assigning Reference Genes and Target-Specific Reaction Efficiency…85
6.9.4.2 Assigning and Naming Control Samples Using the Condition List ……………………87
6.9.4.3 Data Set List …………………………………………………………………………………………….88
6.9.5 Applying an Analysis Method ..................................................................................89
6.9.6 Data Table for Gene Expression Analysis .................................................................89
6.9.7 Graphing Options for Expression Data .....................................................................92
6.9.8 Normalized Expression Calculations.........................................................................96
6.9.9 Relative Quantity Calculations.................................................................................97
6.9.10 Gene Expression - Frequently Asked Questions ......................................................98
6.10 Gene Study: Multi File Gene Expression Analysis ..........................................................99
6.10.1 The Gene Study File.............................................................................................99
6.10.2 Creating a Gene Study File ................................................................................. 101
6.10.3 Gene Expression Study Manager ......................................................................... 102
6.10.4 Editing a Gene Study.......................................................................................... 102
6.10.5 Excluding/Including Samples Using the Gene Expression Plate Interface ...............103
6.10.6 Inter-Run Calibration.......................................................................................... 103
6.11 Post-Run Plate Editing .............................................................................................. 105
6.12 The Reports Tool .....................................................................................................107
6.12.1 Report Viewer Options .......................................................................................108
6.12.2 Parts of the Data Report..................................................................................... 108
6.12.3 Data Analysis Report Types ................................................................................108
Section 7. Calibrating the Instrument........................................................................111
7.1 Calibration Overview ..................................................................................................111