[BioC] Run GOHyperG without specifying a chip

[Robert Gentleman]

Hi,
   Jim is right, but we should split out the different parts, all that 
the chip is used for is to define the universe and it is perfectly 
reasonable to want to define your own universe. Look for some changes in 
the devel arm later this week. One problem with that approach is that we 
will have no way to test that your Entrez Gene IDs are valid, so that is 
going to require that the user take all responsibility on that front 
(and it could have a big effect if you accidently add in a bunch of 
non-Entrez gene ids).

   best wishes
    Robert


James W. MacDonald wrote:
> 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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> 
> 
> 

-- 
Robert Gentleman, PhD
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M2-B876
PO Box 19024
Seattle, Washington 98109-1024
206-667-7700
rgentlem at fhcrc.org