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Hi Paul, Thanks for the bug report, it seems that there is an issue when all values are zero, which shows up intermittently. You can solve it by using try or tryCatch around the call to hyperGTest. You can simply use a p-value of 1, which is what it will be. You should not be loading the GO package for this (KEGG if anything, and even then, please use KEGG.db, not KEGG). I will fix the bug, but given how close the release is I won't back port it, and it will only be available in the devel branch (soon to be the release branch), best wishes Robert Paul Evans wrote: > Hi all, > > I was trying to understand the hyperGTest for KEGG, and used the following code: > > -------------------------------------------------------------------- --------------------------------------- > ## TEST HYPERGTEST FOR KEGG > > library("YEAST") > library("GOstats") > library("GO") > > # Convert to a list > xx <- as.list(YEASTGENENAME) > # Remove probes that do not map to any GENENAME > xx <- xx[!is.na(xx)] > if(length(xx) > 0){ > # Gets the gene names for the first five probe identifiers > xx[1:5] > # Get the first one > xx[[1]] > } > > ## Create gene universe > allGenes <- names(xx) > print(length(allGenes)) > geneUniverse <- allGenes[1:800] > for(i in 1:20){ > ## Create random cluster of 13 genes > geneCluster <- sample(1:800,13,replace=F) > geneCluster <- geneUniverse[geneCluster] > print(i) > print(geneCluster) > params <- new("KEGGHyperGParams", geneIds = geneCluster, > universeGeneIds = geneUniverse, annotation = "YEAST", > pvalueCutoff = 0.1, testDirection = "over") > hgOver <- hyperGTest(params) > dfrm <- summary(hgOver) > #print(dfrm) > } > > -------------------------------------------------------------------- ------------------------------------ > > The output/error that I got is: > > [1] 1 > [1] "YKR067W" "MOF9" "YDR518W" "YPR074C" "YCL011C" "YCR069W" "YDL104C" "YGR136W" "YAR003W" "YFR013W" "YOR116C" "YDR507C" "YGR167W" > [1] 2 > [1] "YJR112W" "CEN8" "YPL005W" "YHR081W" "YLR323C" "YBR131W" "YLR347C" "YHR098C" "YOR107W" "YCL027W" "YNR012W" "CRL16" "YLR329W" > [1] 3 > [1] "YNL327W" "YEL056W" "YNL321W" "YDL111C" "YMR284W" "YLR338W" "YPL008W" "CRL17" "YEL065W" "YFR027W" "YMR269W" "YPL019C" "YML038C" > Error in numW - numWdrawn : non-numeric argument to binary operator > > > [[elided trailing spam]] > > My sessionInfo(): > >> sessionInfo() > R version 2.6.2 (2008-02-08) > i386-pc-mingw32 > locale: > LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States.1252;LC_MONETARY=English_United States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 > attached base packages: > [1] splines tools stats graphics grDevices utils datasets methods base > other attached packages: > [1] KEGG_2.0.1 GOstats_2.4.0 Category_2.4.0 genefilter_1.16.0 survival_2.34 RBGL_1.14.0 GO.db_2.0.2 > [8] graph_1.16.1 goTools_1.10.0 annotate_1.16.1 xtable_1.5-2 AnnotationDbi_1.0.6 RSQLite_0.6-8 DBI_0.2-4 > [15] Biobase_1.16.3 GO_2.0.1 hu6800_2.0.1 hgu95a_2.0.1 hgu95av2_2.0.1 hgu133plus2_2.0.1 hgu133b_2.0.1 > [22] hgu133a_2.0.1 som_0.3-4 YEAST_2.0.1 cluster_1.11.10 > > > thanks! > > > ______________________________________________________________ ______________________ > Looking for last minute shopping deals? > > [[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 > -- Robert Gentleman, PhD Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M2-B876 PO Box 19024 Seattle, Washington 98109-1024 206-667-7700 rgentlem at fhcrc.org