[BioC] hyperGTest

Robert Gentleman rgentlem at fhcrc.org
Mon Oct 13 07:27:20 CEST 2008


Weiwei Shi wrote:
> Hi,
> I am wondering how to get all GO terms (actually for BP category) after I
> run hyperGTest? I need to know what GO terms were checked by hyperGTest.

   That is most easily done by simply finding out how many BP GO terms 
are in the annotation package.  All will be checked, depending a bit on 
your minimum number of genes per term setting, and that too can easily 
be determined from the annotation package.

> BTW, I used summary(x, pvalue=1.1) as a way to find the answer after I run
> hyperGTest for hgu133a, hgu133plus2 and hgu95av2. I found the numbers for
> the three platforms are 637, 637 and 736. I don't know why the databases of
> GO terms are different for the three platforms. I assume they should be the
> same.

   That seems like a bad assumption. Since they have different genes and 
numbers of genes the GO terms associated with those terms also are 
likely to be different.

   best wishes

> Thanks,
> Weiwei

Robert Gentleman, PhD
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M2-B876
PO Box 19024
Seattle, Washington 98109-1024
rgentlem at fhcrc.org

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