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

[James W. MacDonald]

Hi Scott,

Ochsner, Scott A wrote:
> 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 think you could make a convincing argument for either the 45101 or 
24654 probe set groups, but personally I would go with the 45101. My 
rationale would be that all 45101 probe sets were measured, so any of 
them could theoretically have been significant. It doesn't matter IMO 
that some were removed because of low expression rather than a 
statistical test.

HTH,

Jim


> 
> 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
> 
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-- 
James W. MacDonald, M.S.
Biostatistician
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623


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