[BioC] Problem with the function hyperGtest from GOstats package

[Anne.Biton at sanofi-aventis.com]

Thanks James, (sorry for the stupid error!)
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 

Best,

Anne.

-----Message d'origine-----
De : James W. MacDonald [mailto:jmacdon at med.umich.edu] 
Envoyé : jeudi 15 mars 2007 14:19
À : Biton, Anne PH/FR
Cc : bioconductor at stat.math.ethz.ch
Objet : Re: [BioC] Error with the function hyperGtest from GOstats package

Hi Anne,

Anne.Biton at sanofi-aventis.com wrote:
> Dear all,
>  
> I have one subset of GO Ids and one set of Gene EntrezIds.
> I'm trying to perfom an hyperGTest and I want to restrict the 
> annotation to my subset of GO ids.
>  
> So, I define a GOHyperGParams object (I use the slot "catogrySubsetIds"
> to restrict to my GO Ids)
> 
>>params = new ("GOHyperGParams",geneIds = genes, universeGeneIds =
> 
> univers, annotation = "hgu133a", cateogrySubsetIds = GOBPselec)
>  
> where GOBPselec is a vector of GO Ids : 
> 
>>GOBPselec
> 
>  [1] "GO:0006915" "GO:0007165" "GO:0006468" "GO:0006350" "GO:0006508"
> "GO:0008152" "GO:0000004" "GO:0006355" "GO:0006457" "GO:0007242"
> "GO:0006512" ......
> 
> And finally, I launch the test and I have the following error :
> 
>>hg = hyperGTest(params)
> 
> "Error in getGoToProbeMap(go2allprobes, ontology) : 
>         incorrect type of index"
>  
> I know that this error come from "cateogrySubsetIds" but I don't 
> understand why?

I don't think it comes from cateogrySubsetIds, but from the fact that you aren't passing anything in for the 'ontology' slot. Try adding an ontology = "BP" to your call to new("GOHyperGParams", ...).

Best,

Jim


> The description of this slot is :  <<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. >>
>  
> Best regards,
> Anne.
>  
>  
>  
>  
>  
>  
> 
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> 
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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
734-647-5623


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