Hi, Yuan, Alternatively, if you goal is to make the hyperGTest function work on your selected gene, you can either make use of the nsFilter function to filter out the genes that are not annotated to GO term in biological processes or write a simple filter function to do so. The former requires your dataset to be in the form of ExpressionSet. The later can be something like the following (suppose eset if your list of Entrez ID, i.e. eset=c("6310", "10011340")): ontology="BP" Gos <- mget(eset, org.Hs.egGO, ifnotfound=NA) haveGo <- sapply(Gos, function(x) { if (length(x) == 1 && is.na(x)) FALSE else { onts <- Biobase::subListExtract(x, "Ontology", simplify=TRUE) ontology %in% onts }}) eset <- eset[haveGo] On 06/22/10 10:34, James W. MacDonald wrote: > Hi Yu, > > Yuan Jian wrote: >> hello there, >> >> when I run a toy example >>> paramsGO <- new("GOHyperGParams", geneIds = "100113407", >> universeGeneIds = c("6310","100113407"), annotation = >> "org.Hs.eg.db", ontology = "BP", >> pvalueCutoff = 0.05, conditional = FALSE, testDirection = >> "over") >>> hgGO_Over <- hyperGTest(paramsGO) >> I got error below. "Error in getGoToEntrezMap_db(p) : The genes you >> are testing do not have any corresponding GO terms for the ontology >> you are searching." >> >> In my script, geneIDs are generated at runtime. How to make the >> script continue running? >> how to catch the error? > > ?try > ?tryCatch > > Best, > > Jim > > > > >> >> thanks >> YU >> >> >> >> >> >> [[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 > -- Chao-Jen Wong Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Avenue N., M1-B514 PO Box 19024 Seattle, WA 98109 206.667.4485 cwon2 at fhcrc.org