Bio-Rad EXQuest Spot Cutter - Manual (Page 237)

PDQuest User Guide
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Note: If you have Normalization enabled, normalization parameters will be used for
spot quantities. See Section 6.7, Normalization, for further information.
Quantitative Analysis Set Options
The following options help refine the analysis set:
Estimate missing spots: . Otherwise the spot will be reported as missing or
excluded from calculations, as appropriate. This
option is only available on replicate gels and classes.
Estimate saturated spots: If a spot is saturated and therefore cannot be
accurately quantified, an estimate of its value is amde
by fitting a gaussian to the sides of the spot and
extrapolating the peak value on that basis. The
volume is calculated based on the extrapolated
gaussian.
Include qualitative changes: This option includes allows the inclusion of spots
“turned on” in one gel, but “turned off” in the other
based on the minimum fold over background value
you enter.
Note: Estimate missing spots and estimate saturated spots are only available for groups
and classes.
Choose what you wish to compare (gels, replicate gels, or classes, See Section 6.6,
Sample Database, for information on classes) and enter your selections for
comparison (e.g., control gels versus experimental gels).
After you have chosen what to compare, you need to decide what kind of quantitative
changes you want to examine. You can select Above upper limit, Below lower limit,
Between limits, or Outside limits.
Depending on your method choice, the graph to the right changes to reflect the
method. The green portions of the bars correspond to the spots that will be included in
your analysis set.
To view the scatter plot, click the Scatterplot button. Selecting your limits with the
scatterplot is similar to the histogram in that you use the slider bars. The difference