Hi, I was trying to get significant KEGG terms for yeast. Previously, I used the "YEAST" package, but I am now shifting to the "org.Sc.sgd.db" package. A sample of the code, and the error I get is reproduced below: ------------------------------------------------ Begin code ----------------------------------------------------------------- ## TEST HYPERGTEST FOR KEGG #library("YEAST") library("org.Sc.sgd.db") library("GOstats") library("GO") x <- org.Sc.sgdGENENAME # Get the gene names that are mapped to an ORF identifier mapped_genes <- mappedkeys(x) # Convert to a list xx <- as.list(x[mapped_genes]) if(length(xx) > 0) { # Get the GENE NAME for the first five genes xx[1:5] # Get the first one xx[[1]] } ## Create gene universe geneUniverse <- allGenes[3000:4500] 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 = "org.Sc.sgd.db", pvalueCutoff = 0.1, testDirection = "over") hgOver <- hyperGTest(params) dfrm <- summary(hgOver) } -------------------------- End code -------------------------------------- The error I get is: [1] 1 [1] "YJR004C" "YJL108C" "YJL188C" "YIL157C" "YKL039W" "YJR002W" "YIL139C" [8] "YJR024C" "YIR021W" "YJR063W" "YJL166W" "YIR032C" "YKL049C" Error in get(paste(lib, name, sep = "")) : variable "org.Sc.sgdPATH2PROBE" was not found The GO enrichment analysis seems to work fine, it's just the KEGG that seems to cause problems. What am I doing wrong? thanks! PS: sessionInfo is: > sessionInfo() R version 2.8.1 (2008-12-22) 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 [8] methods base other attached packages: [1] org.Sc.sgd.db_2.2.6 YEAST_1.16.0 cairoDevice_2.9-2 [4] yeast2.db_2.2.5 gWidgetsRGtk2_0.0-48 GOstats_2.8.0 [7] Category_2.8.2 genefilter_1.22.0 survival_2.34-1 [10] RBGL_1.18.0 goTools_1.16.0 PFAM.db_2.2.5 [13] KEGG.db_2.2.5 GO.db_2.2.5 org.Mm.eg.db_2.2.6 [16] org.Hs.eg.db_2.2.6 hgug4112a.db_2.2.5 hgug4110b.db_2.2.5 [19] hu6800.db_2.2.5 hgu95a.db_2.2.5 hgu95av2.db_2.2.5 [22] hgu133plus2.db_2.2.5 hgu133b.db_2.2.5 hgu133a.db_2.2.5 [25] RSQLite_0.7-1 DBI_0.2-4 som_0.3-4 [28] yeast.db0_2.2.5 cluster_1.11.12 Rgraphviz_1.14.1 [31] geneplotter_1.20.0 annotate_1.20.1 xtable_1.5-4 [34] AnnotationDbi_1.4.2 lattice_0.17-17 Biobase_2.2.1 [37] graph_1.20.0 gWidgets_0.0-32 loaded via a namespace (and not attached): [1] grid_2.8.1 GSEABase_1.4.0 KernSmooth_2.22-22 RColorBrewer_1.0-2 [5] RGtk2_2.12.7 XML_1.94-0.1 ---------------------------------------------------------------------- ------------------------------------------- [[alternative HTML version deleted]] _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor [[alternative HTML version deleted]]

Hi Paul, It turns out that you are not doing anything wrong. Regrettably, it seems that you were just doing it at the wrong "time". :P I have just checked in a fix for this and it should be propagated through the build system within a day or so. This bug only should have affected the case where you are using KEGG, GOstats and the organism package for yeast. Please let me know if you have any other difficulties and thank you for helping us to improve our code. Marc Paul Evans wrote: > Hi, > > I was trying to get significant KEGG terms for yeast. Previously, I used the "YEAST" package, but I am now shifting to the "org.Sc.sgd.db" package. A sample of the code, and the error I get is reproduced below: > > ------------------------------------------------ Begin code ----------------------------------------------------------------- > ## TEST HYPERGTEST FOR KEGG > > #library("YEAST") > library("org.Sc.sgd.db") > library("GOstats") > library("GO") > > > x <- org.Sc.sgdGENENAME > # Get the gene names that are mapped to an ORF identifier > mapped_genes <- mappedkeys(x) > # Convert to a list > xx <- as.list(x[mapped_genes]) > if(length(xx) > 0) { > # Get the GENE NAME for the first five genes > xx[1:5] > # Get the first one > xx[[1]] > } > > ## Create gene universe > geneUniverse <- allGenes[3000:4500] > > 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 = "org.Sc.sgd.db", > pvalueCutoff = 0.1, testDirection = "over") > hgOver <- hyperGTest(params) > dfrm <- summary(hgOver) > } > > -------------------------- End code -------------------------------------- > > The error I get is: > > [1] 1 > [1] "YJR004C" "YJL108C" "YJL188C" "YIL157C" "YKL039W" "YJR002W" "YIL139C" > [8] "YJR024C" "YIR021W" "YJR063W" "YJL166W" "YIR032C" "YKL049C" > Error in get(paste(lib, name, sep = "")) : > variable "org.Sc.sgdPATH2PROBE" was not found > > > The GO enrichment analysis seems to work fine, it's just the KEGG that seems to cause problems. What am I doing wrong? > > > thanks! > > > > PS: sessionInfo is: > > > >> sessionInfo() >> > > R version 2.8.1 (2008-12-22) > 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 > [8] methods base > > other attached packages: > [1] org.Sc.sgd.db_2.2.6 YEAST_1.16.0 cairoDevice_2.9-2 > [4] yeast2.db_2.2.5 gWidgetsRGtk2_0.0-48 GOstats_2.8.0 > [7] Category_2.8.2 genefilter_1.22.0 survival_2.34-1 > [10] RBGL_1.18.0 goTools_1.16.0 PFAM.db_2.2.5 > [13] KEGG.db_2.2.5 GO.db_2.2.5 org.Mm.eg.db_2.2.6 > [16] org.Hs.eg.db_2.2.6 hgug4112a.db_2.2.5 hgug4110b.db_2.2.5 > [19] hu6800.db_2.2.5 hgu95a.db_2.2.5 hgu95av2.db_2.2.5 > [22] hgu133plus2.db_2.2.5 hgu133b.db_2.2.5 hgu133a.db_2.2.5 > [25] RSQLite_0.7-1 DBI_0.2-4 som_0.3-4 > [28] yeast.db0_2.2.5 cluster_1.11.12 Rgraphviz_1.14.1 > [31] geneplotter_1.20.0 annotate_1.20.1 xtable_1.5-4 > [34] AnnotationDbi_1.4.2 lattice_0.17-17 Biobase_2.2.1 > [37] graph_1.20.0 gWidgets_0.0-32 > > loaded via a namespace (and not attached): > [1] grid_2.8.1 GSEABase_1.4.0 KernSmooth_2.22-22 RColorBrewer_1.0-2 > [5] RGtk2_2.12.7 XML_1.94-0.1 > > > > > -------------------------------------------------------------------- --------------------------------------------- > > > > > [[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 > > > > > [[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 > >