[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]]
> 
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor


-- 
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


**********************************************************
Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues.



More information about the Bioconductor mailing list