Bio-Rad iQ™5 Optical System Software, Version 2.1 User Manual
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Section 6 Data Analysis Module
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Reaction Efficiency and Gene Expression Analysis
Efficiency describes how much of your sequence of interest is being produced with each cycle. An
efficiency value of 100% means that you are doubling your sequence of interest with each cycle.
People focus on efficiency for a number of reasons. There is evidence that using accurate
efficiencies for each of your gene (primer/probe) pairs will give you more accurate results when
using the mathematical modules used in the Gene Expr tab.
You set the efficiency for each of your genes in the Gene List. The default value is 100%. So if no
standards were included on the plate, by default an efficiency value of 100% will be reported.
This efficiency value is fully editable to allow entry of other than a default 100% value
established from previous experiments.
If a standard curve was included on the plate, the software will automatically calculate the
efficiency for that gene and report it in the Efficiency (%) column. To use Auto Efficiency, you
must have standards in your experiment that result in valid standard curves in the PCR Quant
tab. The iQ5 software only requires two standards at different concentrations, though it is
recommended to have at least four samples in triplicate across a relevant dynamic range.
6.9.4.2 Assigning and Naming Control Samples Using the Condition List
When the Settings button is active and Condition List is selected, the conditions being analyzed in
the experiment are listed along with their full name. This Full Name column is editable so that
longer more descriptive names may be entered if your Condition Name entry was abbreviated.
NOTE: Condition Name entries have a character entry limit of 15 characters.
The Condition List option represents particular tests or treatments being evaluated for the
purposes of your experiment. A condition can be as simple as “sample 1” or complex as “mouse
#123558 liver + PMA”, though the latter example is often too long to present on a graph.
You can view conditions as samples in the Condition List spreadsheet as shown in Figure 6.44.
Fig. 6.44. The Condition List.