Dear list, I am making a get set enrichment analysis, my commands are : library(biomaRt) #list to test broilers_HT.test<- broilers_HT$entrezgene #now I define my universe as all the entrezgenes all <- total_data_u$entrezgene # in your case, it's not all the entrezgenes, but those corresponding to the ensembl_gene_id included in your analysis # if you have problem with this, contact me then # now the regular GOstats testing library(GOstats) library(multtest) library(org.Hs.eg.db) ont = c("BP") options(digits=3) params_temp = new("GOHyperGParams", geneIds= broilers_HT.test, universeGeneIds=all, annotation="org.Hs.eg.db", ontology=ont, pvalueCutoff=1, conditional = TRUE, testDirection = "over") hGT = hyperGTest(params_temp) #ps1 <- probeSetSummary(hGT, 0.05, 5) result <- summary(hGT) pval = result$Pvalue ## add FDR info library(multtest) FDRpval = mt.rawp2adjp( pval , c("Bonferroni","BH", "BY")) GO.resultbroilers_HT2 <- cbind(result,FDRpval$adjp) this has worked well before and now I am getting the following error: Error in .checkKeys(value, Lkeys(x), x@ifnotfound) : value for "GO:0010817" not found the difference is that I have updated my linux distribution, befor I had Unbuntu 9.04 and now I have 9.10 and after that I had to reinstall all the bioconductor packages, like biomart GOstats, multtest and org.Hs.eg.db can someone help me? thanks Andreia [[alternative HTML version deleted]]

Hi Andreia, Andreia Fonseca wrote: > Dear list, > > I am making a get set enrichment analysis, my commands are : > > library(biomaRt) > > #list to test > broilers_HT.test<- broilers_HT$entrezgene > #now I define my universe as all the entrezgenes > all <- total_data_u$entrezgene > # in your case, it's not all the entrezgenes, but those corresponding to the > ensembl_gene_id included in your analysis > # if you have problem with this, contact me then > > > > # now the regular GOstats testing > library(GOstats) > library(multtest) > library(org.Hs.eg.db) > > ont = c("BP") > options(digits=3) > > params_temp = new("GOHyperGParams", geneIds= broilers_HT.test, > universeGeneIds=all, > annotation="org.Hs.eg.db", ontology=ont, > pvalueCutoff=1, conditional = TRUE, > testDirection = "over") > hGT = hyperGTest(params_temp) > #ps1 <- probeSetSummary(hGT, 0.05, 5) > result <- summary(hGT) > pval = result$Pvalue ## add FDR info > library(multtest) > FDRpval = mt.rawp2adjp( pval , c("Bonferroni","BH", "BY")) > GO.resultbroilers_HT2 <- cbind(result,FDRpval$adjp) > > this has worked well before and now I am getting the following error: > > Error in .checkKeys(value, Lkeys(x), x at ifnotfound) : value for > "GO:0010817" not found > > the difference is that I have updated my linux distribution, befor I had > Unbuntu 9.04 and now I have 9.10 and after that I had to reinstall all the > bioconductor packages, like biomart GOstats, multtest and org.Hs.eg.db Please supply the output from sessionInfo(). Also, you have omitted exactly how you got the Entrez Gene IDs. Please supply that code as well. In addition, please give us your input and output straight from the R console rather than collapsing it as you have. The error couldn't have come from the call to cbind(), so mixing up the order of the code and resulting error makes it even harder to help you. Best, Jim > > can someone help me? > > thanks > Andreia > > [[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 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues