[BioC] Run GOHyperG without specifying a chip

[James W. MacDonald]

knaxerov at ix.urz.uni-heidelberg.de wrote:
> Hello everyone,
> 
> here's a really trivial question, but I can't find the answer anywhere: can I
> use GOHyperG() in GOstats without specifying a particular microarray chip? I'd
> simply like to pass a list of EntrezGene IDs as my "total population".

No, GOHyperG() requires an annotation package to extract all the GO IDs 
for each probe on the chip.

Although it is a non-trivial task, you might consider building an 
annotation package based on your vector of Entrez Gene IDs. This can 
substantially simplify further annotation of results from your 
microarray data.

Best,

Jim


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