[BioC] GOstats with yeast2

[Robert Gentleman]

Hi Sebastien,
   There is no requirement that I am aware of for ENTREZIDs. All that is 
required is that you have some set of indentifiers (in this case yeast 
standard names seem most likely) that map to KEGG. And yeast2.db does 
seem to satisfy that requirement so I expect it would simply work.
Perhaps you could show what you tried, what happened and your sessionInfo?


   best wishes
    Robert


Sebastien Gerega wrote:
> Hi,
> what is the best way to use GOstats (specifically a hyperG test on KEGG) 
> with the yeast2.db annotation? I have looked around the mailing list 
> archive and the fact that yeast2.db doesn't have a yeast2ENTREZID 
> environment has been mentioned several times. However, I haven't managed 
> to find any mention of how to get around this and use the annotation 
> with GOstats.
> thanks,
> Sebastien
> 
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-- 
Robert Gentleman, PhD
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
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rgentlem at fhcrc.org