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Hi Dongxiao, Zhu, Dongxiao wrote: > Hi, I am trying to use Gostats to calculate enrichment or depletion of > GO terms. The below is the code adapted from vignette. Assume we start > from a mouse 4302 expressionset object "exprSet1000". It always returns > empty table no matter what data I try. > > Can somebody help me out? Yes. If you look at the code below, you will notice that your geneIds are identical to your universeGeneIds. I don't think this makes any sense - you want the geneIds to be a subset of your universeGeneIds (which technically I guess they are, so you want a subset where geneIds < universeGeneIds). Best, Jim > > Thanks. > > ## General Filtering, remove probe sets without Entrez ID > entrezIds <- mget(featureNames(exprSet1000), envir = mouse4302ENTREZID) > haveEntrezId <- names(entrezIds)[sapply(entrezIds, function(x) > !is.na(x))] > numNoEntrezId <- length(featureNames(exprSet1000)) - > length(haveEntrezId) > bcrAblOrNeg <- exprSet1000[haveEntrezId, ] > > ## Remove probe sets for which we have no GO annotation. > haveGo <- sapply(mget(featureNames(bcrAblOrNeg), mouse4302GO), > function(x) { > if (length(x) == 1 && is.na(x)) > FALSE > else TRUE > }) > numNoGO <- sum(!haveGo) > bcrAblOrNeg <- bcrAblOrNeg[haveGo, ] > > ## remove redundant probe set ids > bcrAblOrNegIqr <- apply(exprs(bcrAblOrNeg), 1, IQR) > numNsWithDups <- length(featureNames(bcrAblOrNeg)) > uniqGenes <- findLargest(featureNames(bcrAblOrNeg), bcrAblOrNegIqr, > "mouse4302") > bcrAblOrNeg <- bcrAblOrNeg[uniqGenes, ] > > entrezUniverse <- unlist(mget(featureNames(bcrAblOrNeg), > mouse4302ENTREZID)) > if (any(duplicated(entrezUniverse))) stop("error in gene universe: can't > have duplicate Entrez") > selectedEntrezIds <- unlist(mget(featureNames(bcrAblOrNeg), > mouse4302ENTREZID)) > > hgCutoff <- 1 > params <- new("GOHyperGParams", geneIds = selectedEntrezIds, > universeGeneIds = entrezUniverse, annotation = "mouse4302", > ontology = "BP", pvalueCutoff = hgCutoff, conditional = FALSE, > testDirection = "over") > > paramsCond <- params > conditional(paramsCond) <- TRUE > hgOver <- hyperGTest(params) > hgCondOver <- hyperGTest(paramsCond) > > > > ------------------------------------------------- > Dongxiao Zhu > Stowers Institute for Medical Research > Phone: 816-926-4456 > FAX: 816-926-4674 > > > [[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 Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues.