[BioC] how to get gene list after hyperGTest

[James W. MacDonald]

Yue, Chen - BMD wrote:
> Hi,
> 
> I'm wondering if someone can help me with the result extraction after
> hyperGTest in GOstats package. After I obtained the hyperGTest
> result, I also want to know what category each input gene associates
> with, for example a KEGG pathway. What function should I use? Or
> should I use another package?

It's not clear what you want here. As Elmar Bucher shows in another 
email, you can use the KEGG.db package directly to get the information 
you want.

However, this question is reminiscent of a question I have had in the 
past. Namely, which genes (reporters) are associated with a given 
GO/KEGG pathway that was found significant in a Fisher's exact test.

To answer this question, you want the probeSetSummary() function in the 
GOstats package.

Best,

Jim


> 
> Thanks!
> 
> Chen, Yue
> 
> 
> 
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-- 
James W. MacDonald, M.S.
Biostatistician
Douglas Lab
University of Michigan
Department of Human Genetics
5912 Buhl
1241 E. Catherine St.
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