Hi, Before my performing this GO analysis, the 3 arrays' probes have been mapped to entrezgene ids (..... mapping between affy's probes and RefeSeqs by blasting probe sequence against human refseq sequence database. And every refseq id were then mapped to gene name of EntrezID based on Gene database of NCBI.... It was done by my collaborator). And the differences between the three have been removed. So the input to hyperGTest are the same; however, I believe I should not use hyperGTest here since this function goes back to use array-specific mappings; and thus the numbers of GO terms are different from each other, I assume. Best, Weiwei On Mon, Oct 13, 2008 at 1:27 PM, Robert Gentleman <rgentlem@fhcrc.org>wrote: > Hi, > > 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 > Robert > > >> 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 > 206-667-7700 > rgentlem@fhcrc.org > -- Weiwei Shi, Ph.D Research Scientist GeneGO, Inc. "Did you always know?" "No, I did not. But I believed..." ---Matrix III [[alternative HTML version deleted]]