[BioC] Problem with the function hyperGtest from GOstats package

[James W. MacDonald]

Hi Anne,

Anne.Biton at sanofi-aventis.com wrote:
> Thanks James, (sorry for the stupid error!)

No problem. I make at least one per day ;-D

> In fact, now I return to my first problem : the slot catogrySubsetIds isn't taken into account : the annotation seems to be done on all GO Ids in the two cases :
> 
> 
>>params = new ("GOHyperGParams",geneIds = genes, universeGeneIds = univers, annotation = "hgu133a", ontology = "BP")
>>hgtest = hyperGTest(params)
>>params = new ("GOHyperGParams",geneIds = genes, universeGeneIds = univers, annotation = "hgu133a", ontology = "BP",cateogrySubsetIds = GOBPselec)
>>hgtest2 = hyperGTest(params)
>>hgtest2
> 
> Gene to GO BP  test for over-representation 
> 566 GO BP ids tested (11 have p < 0.01)
> Selected gene set size: 155 
>     Gene universe size: 7620 
>     Annotation package: hgu133a 
> 
>>hgtest
> 
> Gene to GO BP  test for over-representation 
> 566 GO BP ids tested (11 have p < 0.01)
> Selected gene set size: 155 
>     Gene universe size: 7620 
>     Annotation package: hgu133a 

As you already noted, the man page states

'cateogrySubsetIds': Object of class '"ANY"': If the test method
           supports it, can be used to specify a subset of category ids
           to include in the test instead of all possible category ids.

I don't know which test method supports this argument, but apparently 
hyperGTest() doesn't.

Best,

Jim

> 
> Best,
> 
> Anne.
> 


-- 
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
734-647-5623


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