[BioC] GOstats : Error in getUniverseHelper - No Entrez Gene ids left in universe

[Robert Gentleman]

Hi Ben,
   First you should update your R (2.9.1 is the current release).
Next, it looks like the IDs in your universe might not be correct (or 
something of that nature). Are you sure they are EG IDs - they don't 
look like they are.

   best wishes
    Robert


Benoit Ballester wrote:
> Hi,
> 
> I am getting this error when I run hyperGTest from GOstats. Any idea on 
> what is going wrong would be appreciated ?
> 
> R version 2.8.1 (2008-12-22)
> GOstats  1.7.4
> I am also attaching the files genefile/universe.txt
> 
> write.table(ori$Accession, "universe.txt", sep = "\t", 
> quote=FALSE,row.names=FALSE,col.names=FALSE)
> 
> geneFile  <- "genefile.txt"
> uniFile   <- "universe.txt"
> 
> universe  <- scan(uniFile, what="character")
> genelist  <- scan(geneFile, what="character")
> 
> pcut    <- 0.05
> catSize <- 5
> 
> 
> params    <- new("GOHyperGParams", geneIds=genelist, 
> universeGeneIds=universe,
>               annotation="org.Mm.eg", ontology="BP", pvalueCutoff=pcut,
>               conditional=FALSE, testDirection="over")
> 
> 
> results <- hyperGTest(params)
> Error in getUniverseHelper(probes, datPkg, entrezIds) :
>   No Entrez Gene ids left in universe
> 
> 
> 
> 
> Thanks,
> 
> Ben
> 
> 
> 
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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, M1-B514
PO Box 19024
Seattle, Washington 98109-1024
206-667-7700
rgentlem at fhcrc.org