hyperGTest(paramsGO)
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Yuan Jian ▴ 250
@yuan-jian-2603
Last seen 8.8 years ago
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? thanks YU [[alternative HTML version deleted]]
Annotation GO Annotation GO • 1.9k views
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@james-w-macdonald-5106
Last seen 6 hours ago
United States
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 -- James W. MacDonald, M.S. Biostatistician Douglas Lab University of Michigan Department of Human Genetics 5912 Buhl 1241 E. Catherine St. Ann Arbor MI 48109-5618 734-615-7826 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues
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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
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