Bio-Rad EXQuest Spot Cutter - Manual (Page 219)

PDQuest User Guide
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This model is useful if you want to correct for known variations in samples across
gels (e.g., the amount of cells that went into an experiment, the amount of extract
loaded, the length of time the images were detected, etc.).
Counts Loaded from Gel Record
In this method, the raw quantity of each spot in a member gel is divided by the total
counts loaded into that gel, as specified in the Gel Record when you performed
calibration.
Note: This method is only available if you have performed calibration on your
MatchSet gels. (See Appendix J.)
The counts loaded in each gel are listed in the table at the bottom of the Normalization
dialog; this value will be used as the denominator in the normalization formula. Select
the Counts Loaded from Gel Record option button to activate this normalization
method.
This method assumes that few protein spots change within the experiment, and that
the changes average out across the whole gel. This model can be useful if you want to
correct for known variations in the amount of sample loaded across gels, as measured
prior to loading with a scintillation counter.
If you select this method, you can compensate for pipetting errors in all MatchSet
members by selecting the Pipetting Error Compensation checkbox.
Pipetting Error Compensation
When this checkbox is selected, the software will attempt to correct for minor
systematic errors inherent in scintillation counting, pipetting, and exposing films. The
normalization process is based on the assumption that these minor errors affect all
proteins equally. It also assumes that few protein spots change within the experiment
or that when changes do occur, they do not alter the random distribution from one
sample to the next.
When you select this checkbox, a pop-up box will display the calculated
compensation value for each MatchSet member. These values will also appear in the
in the table at the bottom of the Normalize dialog.