Software, Version 2.1 Owner's manual

Section 2 Quick Guides
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2. Select a data file from the file tree browser, and then click Analyze. The file opens in the
PCR Quant tab within the Data Analysis module.
3. Select or deselect wells to be included in the analysis by selecting Analyze Wells. Select
or deselect wells to be displayed by selecting Display Wells.
4. The iQ5 software automatically chooses the data analysis conditions including baselines
and thresholds. If the data file is being opened for the first time, an automated analysis
of baselines and threshold will be conducted, including every defined well. If the file was
previously saved after an analysis, the last set of analysis conditions are applied again.
5. Make any manual adjustments to the threshold by clicking and dragging the green
threshold line.
6. Make any manual adjustments to the baseline by right-clicking on the amplification traces
plot to access the baseline threshold parameters popup window and editing User Defined
options.
NOTE: You can revert to software auto calculated threshold and baseline by right-
clicking on the amplification traces plot to access the baseline threshold parameters
popup window and selecting Auto Calculated.
2.4.2 End Point Quick Guide
You can implement End Point analysis in two ways:
• Click Run End Point to initiate the collection of End Point data from a sample plate
• Click the End Point tab in the Data Analysis module for an existing data file
Initiating an End Point Run
1. Insert the experimental plate into the iCycler reaction module.
2. From the Workshop Setup Window Select or Create the Plate Setup from the Plate Setup
tab.
3. Click Run End Point.
4. Check that the desired Protocol and Plate Setup are displayed in the bottom half of the
Initiate Run screen.
5. In the Run-Time Central/Initiate Run tab, specify the setpoint for data collection, and
then click Begin Run.
NOTE: You must use Persistent Well Factors for every End Point Run.
6. Name the file with a unique name in the Save Optical Data File dialog box, and then click
Save.
End Point Analysis of an Newly Completed End Point Run
1. Once the real-time PCR detection system completes the run, the End Point tab is
displayed.
2. Make selections for the following parameters:
• Method — Use Negatives to differentiate samples that do not amplify the target
sequence from those that do amplify the target sequence.
• End Point Tolerance and Tolerance Parameter.