[BioC] Which genes are in the GO count column?

[James W. MacDonald]

Hi Ingrid,

Ingrid H. G. Østensen wrote:
> Hi
> 
> I am testing for GO in my dataset and I am able to make html pages
> that contains different type of information. But I was wondering if
> there is some way to find out which genes are in the Count column? It
> might say 2, but not which 2 genes.

See probeSetSummary() in GOstats and hyperG2annaffy() in affycoretools. 
Note that for probeSetSummary() to work correctly you have to pass in a 
*named* vector of Entrez Gene IDs, which you can get by using unlist():

my.named.probeids <- unlist(mget(probeID.vector, 
"chip.annotation.package.name"))

Best,

Jim


> 
> Regards, Ingrid
> 
> [[alternative HTML version deleted]]
> 
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-- 
James W. MacDonald, M.S.
Biostatistician
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
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