Bio-Rad iQ™5 Optical System Software, Version 2.1 - Manual (Page 61)

Section 6 Data Analysis Module
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Removing wells from data analysis changes the calculation of the threshold location. Changing
the calculation of the threshold location may result in a change in the threshold crossing (C
T
)
location, thus affecting all subsequent data analyses that depend on C
T
values. This would
include standard curve calculations and quantification of unknowns, gene expression, and allelic
discrimination using threshold crossing values.
In addition, removing wells from analysis will change the statistics for replicates.
To select the wells to include in data analysis:
1. In the PCR Quant tab, click Analyze Wells. The Select Wells to Analyze floating window
appears. A set of fluorophore selector buttons appears at the top of this window. When
you click a fluorophore button, the sample type present in that well for that fluorophore
is colored.
2. To select or deselect an individual well, click inside that well. Wells included in the
analysis appear with a yellow and black border. Wells excluded from the analysis appear
with a pale border. When a well is excluded from analysis, all fluorophores in that well
are excluded.
3. To select all wells, click Select All.
4. To toggle the current selection so all wells currently selected will be unselected and vice
versa, click the uppermost left cell of the spreadsheet; this cell has the color of the
currently selected fluorophore. You can also perform this action on a subset of the
spreadsheet by clicking the appropriate row or column header. Only the wells in that row
or column are toggled.
5. After you determine which wells to include in analysis, click Apply if you want the Select
Wells to Analyze window to remain open after the iQ5 software re-analyzes the wells. If
you are satisfied with your selection, click OK to close the dialog box and update the
wells to include in the analysis. If you click Cancel, the iQ5 software closes the dialog box
and discards all changes.
NOTE: This procedure does not permanently remove data. This procedure only removes that
data from the current analysis. You can add the excluded wells back to the analysis at any time
by including them in the Select Wells to Analyze dialog box.
Display Wells
Click the Display Wells button on the PCR Quant screen to select the wells that you wish to
include in the data display.
After you click Display Wells, the Select Analyzed Wells for Display floating window appears, as
shown below in Figure 6.6.
You can include or exclude wells for display in the Select Analyzed Wells for Display floating
window. You can only choose from analyzed wells. Wells that have been excluded from analysis
in the Select Wells to Analyze window do not appear in the Select Analyzed Wells for Display
window.
Selecting wells for display does not change the underlying data analysis. Therefore, the
calculation of thresholds and replicate statistics does not change.