GOstats : Error in getUniverseHelper - No Entrez Gene ids left in universe
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@benoit-ballester-2259
Last seen 9.6 years ago
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$Accession, "universe.txt", sep = "\t", quote=FALSE,row.names=FALSE,col.names=FALSE) geneFile <- "genefile.txt" uniFile <- "universe.txt" universe <- scan(uniFile, what="character") genelist <- scan(geneFile, what="character") pcut <- 0.05 catSize <- 5 params <- new("GOHyperGParams", geneIds=genelist, universeGeneIds=universe, annotation="org.Mm.eg", ontology="BP", pvalueCutoff=pcut, conditional=FALSE, testDirection="over") results <- hyperGTest(params) Error in getUniverseHelper(probes, datPkg, entrezIds) : No Entrez Gene ids left in universe Thanks, Ben -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: universe.txt URL: <https: stat.ethz.ch="" pipermail="" bioconductor="" attachments="" 20090805="" f4ee67fb="" attachment.txt=""> -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: genefile.txt URL: <https: stat.ethz.ch="" pipermail="" bioconductor="" attachments="" 20090805="" f4ee67fb="" attachment-0001.txt="">
GOstats GOstats • 1.4k views
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rgentleman ★ 5.5k
@rgentleman-7725
Last seen 8.9 years ago
United States
Hi Ben, First you should update your R (2.9.1 is the current release). Next, it looks like the IDs in your universe might not be correct (or something of that nature). Are you sure they are EG IDs - they don't look like they are. best wishes Robert Benoit Ballester wrote: > Hi, > > I am getting this error when I run hyperGTest from GOstats. Any idea on > what is going wrong would be appreciated ? > > R version 2.8.1 (2008-12-22) > GOstats 1.7.4 > I am also attaching the files genefile/universe.txt > > write.table(ori$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 > > > > -------------------------------------------------------------------- ---- > > _______________________________________________ > 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 -- 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
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Marc Carlson ★ 7.2k
@marc-carlson-2264
Last seen 7.7 years ago
United States
Hi Benoit, This error basically means that after filtering, there were no Entrez Gene IDs left to test on. Newer versions of this software have more friendly messages, but there many things that can go wrong with your inputs that could have caused this. You might want to look at your values for genelist and universe and make sure that those are valid entrez gene IDs etc. Marc 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") pmnn > > 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 > > > -------------------------------------------------------------------- ---- > > _______________________________________________ > 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
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Hi Benoit, One more thing that might help you is the new AnnotationDbi vignette which should demonstrate how you could convert those refseq IDs into entrez gene IDs. The org.Mm.egREFSEQ mapping in the org.Mm.eg.db package should have the information that you need. You can read the very latest version of this document here: http://www.bioconductor.org/packages/devel/bioc/vignettes/AnnotationDb i/inst/doc/AnnotationDbi.pdf Marc Marc Carlson wrote: > Hi Benoit, > > This error basically means that after filtering, there were no Entrez > Gene IDs left to test on. Newer versions of this software have more > friendly messages, but there many things that can go wrong with your > inputs that could have caused this. You might want to look at your > values for genelist and universe and make sure that those are valid > entrez gene IDs etc. > > Marc > > > > > > 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") pmnn >> >> 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 >> >> >> ------------------------------------------------------------------- ----- >> >> _______________________________________________ >> 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 >> > > _______________________________________________ > 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 > >
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Heidi Dvinge ★ 2.0k
@heidi-dvinge-2195
Last seen 9.6 years ago
Hi Ben, your IDs are RefSeq, and org.Mm.eg.db expects Entrez Gene (the "eg" part of the package name). Try converting them with "org.Mm.egREFSEQ2EG" first. Cheers \Heidi > 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 > > > _______________________________________________ > 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
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@manca-marco-path-3578
Last seen 9.6 years ago
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: mercoled? 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
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