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

[Manca Marco (PATH)]

Hi Benoit,

I am not an expert (by any means) here, but having a glance at the files you are attaching I notice that they are Genebank identifiers (and not Entrez) and that they are still with the NM_*****.* format, where .* is the version of the record. Now I have read somewhere (it could even be the vignette of GOstats but I don't remember) that you should remove the .* part of your identifier, which adds no information to your GOstats elaboration and could turn into some troubles during the job (even though I have no clue whether this is the case here). Anyway, people more expert than me can amend my suggestion, but I would try this correction.

Hope this help. Best regards,
Marco

--
Marco Manca, MD
University of Maastricht
Faculty of Health, Medicine and Life Sciences (FHML)
Cardiovascular Research Institute (CARIM)
E-mail: m.manca at path.unimaas.nl
Mobile: +31626441205
Twitter: @markomanka
________________________________________
Da: bioconductor-bounces at stat.math.ethz.ch [bioconductor-bounces at stat.math.ethz.ch] per conto di Benoit Ballester [benoit at ebi.ac.uk]
Inviato: mercoledì 5 agosto 2009 13.35
A: bioconductor at stat.math.ethz.ch
Oggetto: [BioC] GOstats : Error in getUniverseHelper - No Entrez Gene ids left in universe

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