Hi community, I would like to compute Kolmogorov-Smirnov like tests. I built a TopGOobject with custom annotations and predefined list of interesting genes (those having logFC larger than a chosen threshold). Could you please suggest me how to add logFC values to my TopGO object? Here is the code I have so far. I've been able to run FisherTest and want to try now Kolmogorov-Smirnov and compare outputs: Thanks, Bernardo #################cellular component################################################### library(topGO) geneID2GO <- readMappings(file = "annot_wego_20131028_1232_HPNK_3.txt", sep= "\t", IDsep = ",") str(head(geneID2GO)) geneNames <- names(geneID2GO) head(geneNames) x <- read.csv("DEG", header = TRUE) myInterestingGenes <- as.vector(x$genes) geneList <- factor(as.integer(geneNames %in% myInterestingGenes)) names(geneList) <- geneNames str(geneList) GOdata <- new("topGOdata", ontology = "CC", allGenes = geneList, annot = annFUN.gene2GO, gene2GO = geneID2GO) GOdata test.stat <- new("classicCount", testStatistic = GOFisherTest, name = "Fisher test") resultFisher <- getSigGroups(GOdata, test.stat) resultFisher resultFis <- runTest(GOdata, algorithm = "classic", statistic = "fisher") pvalFis <- score(resultFis) head(pvalFis) geneData(resultFis) pvalFis <- score(resultFis) hist(pvalFis, 50, xlab = "p-values") dev.copy2pdf(file = "P-value_CC.pdf") #Save as .pdf allRes <- GenTable(GOdata, classic = resultFis, orderBy = "classic", ranksOf= "classic", topNodes = 100) allRes write.table(allRes, "Fisher_CC.txt", sep="\t") -- *Bernardo Bello Ortí* PhD student CReSA-IRTA Campus de Bellaterra-Universitat Autònoma de Barcelona Edifici CReSA 08193 Bellaterra (Barcelona, Spain) Tel.: 647 42 52 63 *www.cresa.es * * * [[alternative HTML version deleted]]