GOstats: hyperGTest for KEGG with org.Sc.sgd.db
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Paul Evans ▴ 180
Last seen 7.4 years ago
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]]
Annotation GO Yeast hgu133a hgu133b hgu133plus2 hgu95a hgu95av2 hgug4110b hgug4112a GO • 805 views

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