[BioC] Question about the appropriate uniververse for GOHyperG or hyperGtable

[Ochsner, Scott A]

Hello BioC,

I have a list of 1164 differentially expressed probe sets extracted from an experiment done with mouse4302 chips. To arrive at the list I first filtered log2 expression values by removing those below a log2 of 6.  This left me with 24654 probe sets from 45101.  Next I used limma to model treatment
effects and used an fdr adjusted fit2$F.p.value to extract those genes displaying differential expression in at least one of two contrasts (p<0.001).  This left me with 2612 probe sets.  My list of 1164 probe sets are those probe sets which are upregulated in both contrasts within the significant
set of 2612.  I would like to use GOHyperG or hyperGtable to evaluate overrepresented BP GO terms within the 1164 list.  Should my BP GO universe come from the 45101, 24654, or 2612 probe set groups?

I hope this is clear,

Thanks for any help,   

Scott A. Ochsner, Ph.D.
Baylor College of Medicine
One Baylor Plaza, N810
Houston, TX. 77030
lab phone:  713-798-1620
office phone:  713-798-1585
fax:  713-798-4161