Bio-Rad Firmware & Software Updates - Manual (Page 135)

Gene Expression Analysis
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Table 42. Information in the Results tab.
NOTE: Data for replicates are found only in the spreadsheets of data analysis tabs
in which Split Out Replicates has been selected (that is, Clustergram and Heat
Map); There may be a discrepancy between expression data in the gene
expression analysis spreadsheets if “none” is selected for the bar chart Control
Sample.
Gene Study
Create a Gene Study to compare gene expression data from one or more real-time PCR
experiments using an inter-run calibrator to normalize between the experiments. Create a
Gene Study by adding data from one or more data files (.pcrd extension) to the Gene Study;
the software groups them into a single file (.mgxd extension).
NOTE: The maximum number of samples you can analyze in a Gene Study is
limited by the size of the computer's RAM and virtual memory.
Gene Study Inter-Run Calibration
Inter-run calibration is automatically attempted in every Gene Study for each target to
normalize inter-run variations between targets assayed in separate real-time PCR runs (that is,
different .pcrd files generated from different plates).
For the software to recognize a sample as an inter-run calibrator, it must share matching target
name, sample name, and if used, biological set name across every plate being compared.
NOTE: At least one inter-run calibrator sample must be present in the Gene Study
for inter-run calibration to occur. Targets without appropriate inter-run calibrator
samples will be processed without correction in the Gene Study (not
recommended).
Inter-run calibrators can be applied in two ways:
1. Per target: different PCR primers can have different efficiency. By default the inter-run
calibrator is applied to all of the wells on the same plate that have the same target name, i.e.
Cq generated with the same assay.
Information Description
Target Target name (amplified gene)
Sample Sample name
Mean Cq Mean of the quantification cycle
Mean Efficiency Corrected Cq Mean of the quantification cycle after adjusting for the reaction
efficiency
Normalized Expression Target expression normalized to a reference target (
ΔΔC
q
)
Relative Normalized
Expression Normalized expression relative to a control sample. Also called
Fold Change
Regulation Change in expression relative to a control sample
Compared to Regulation
Threshold Up- or downregulation of an experimental sample based on
the threshold setting
P-Value The probability that a difference in expression is significant
Exceeds P-Value Threshold Indication of whether or not the P value for a target exceeds a
threshold