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

[Seth Falcon]

"James W. MacDonald" <jmacdon at med.umich.edu> writes:

> 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"))

So assuming the OP is using GOstats, R-2.5.x, and the latest available
version installed using biocLite...

  Please try

       help("HyperGResult-accessors")

+ seth

-- 
Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center
BioC: http://bioconductor.org/
Blog: http://userprimary.net/user/