[BioC] Error with the function hyperGtest from GOstats package
James W. MacDonald
jmacdon at med.umich.edu
Thu Mar 15 14:18:53 CET 2007
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.
>
>
>
>
>
>
>
> [[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
734-647-5623
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