D quantitative analysis sets – Bio-Rad EXQuest Spot Cutter User Manual
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PDQuest User Guide
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must be detected in >50% of the gels in the group to
be included. This is important in qualitative analysis
because the analysis is based on whether spots appear
in one group or class and do not appear in another.
Estimate saturated spots:
This option estimates the total peak value for a
saturated spot.
Note:
These options are only available for groups and classes.
Choose whether to compare gels, replicate gels, or classes (See Section 6.6, Sample
Database, for information on classes). Select the items you want to compare. If you
click A the pop-up box displays a list available for analysis. Select what you want to
compare from the list and their names display in the A or B field.
Now select whether you want to highlight spots that were on in A/off in B (On in A)
or on in B/off in A (On in B).
Finally, you need to tell PDQuest what “turned on” or “turned off” means. How many
times greater than the minimum detectable spot should the quantitation be for a spot
to be included in this analysis set? Should it be ten-fold greater than the minimum? If
so, enter 10.00 next to the Fold over minimum sensitivity prompt.
Click on the Save button at the bottom of the dialog box to add the analysis set to the
ASM.
Be sure to enter a name for the set. If you forget, a pop-up box will remind you to do
so.
As with all other types of analysis sets, when the Analysis Set Template is open, you
can view the results in the MatchSet immediately. To the right of the dialog, you can
specify the spot marker, on which gel(s) to show the spots, and what information to
show on the gel(s).
When you open the Analysis set Template, whatever analysis sets you have selected
in the ASM become inactive. To view these sets in the Analysis set Template, check
the box labeled, “Display Selected sets.”
7.1.d Quantitative Analysis Sets
Quantitative analysis sets allow you to perform fold change analyses. To create a
Quantitative Analysis Set, select Quantitative from the Select Set Type dialog.