topGO expected values showing NA
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@kishor-tappita-2563
Last seen 7.8 years ago
Dear Bioconductor Users, I am trying to find enriched GO terms using topGO. I am using Weight01 algorithm for finding the enrichment. I get significantly enriched GO Terms but I see an NA value in the expected column. Below is the code I am using. Please help me with solving the NA issue. sampleGOdata <- new("topGOdata", description = "Simple session", ontology = "BP",allGenes = geneList, geneSel = topDiffGenes,nodeSize = 10,annot = annFUN.db,affyLib= "hgu133plus2.db") resultFisher <- runTest(sampleGOdata, algorithm = "classic", statistic = "fisher") resultWeight01 <- runTest(sampleGOdata, algorithm ="weight01", statistic = "fisher") allRes <- GenTable(sampleGOdata, classicFisher = resultFisher,weight01=resultWeight01,orderBy = "weight01", ranksOf = "classicFisher", topNodes = 100,numChar=200) topDiffGenes <- function(Score) { return(Score < 0.05) } Thanks, Kishor > sessionInfo() R version 2.15.1 (2012-06-22) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_SG LC_NUMERIC=C LC_TIME=en_SG [4] LC_COLLATE=en_SG LC_MONETARY=en_SG LC_MESSAGES=en_SG [7] LC_PAPER=C LC_NAME=C LC_ADDRESS=C [10] LC_TELEPHONE=C LC_MEASUREMENT=en_SG LC_IDENTIFICATION=C attached base packages: [1] grid stats4 splines stats graphics grDevices utils [8] datasets methods base other attached packages: [1] hgu133plus2.db_2.8.0 org.Hs.eg.db_2.8.0 Rgraphviz_2.2.1 [4] BiocInstaller_1.8.3 topGO_2.10.0 SparseM_0.96 [7] GO.db_2.8.0 RSQLite_0.11.2 DBI_0.2-5 [10] AnnotationDbi_1.20.5 Biobase_2.18.0 BiocGenerics_0.4.0 [13] graph_1.36.2 multicore_0.1-7 coin_1.0-21 [16] modeltools_0.2-19 mvtnorm_0.9-9994 survival_2.36-14 [19] samr_2.0 matrixStats_0.6.2 impute_1.32.0 loaded via a namespace (and not attached): [1] IRanges_1.16.6 lattice_0.20-6 parallel_2.15.1 R.methodsS3_1.4.2 [5] tools_2.15.1 [[alternative HTML version deleted]]
GO hgu133plus2 topGO GO hgu133plus2 topGO • 1.2k views
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@palmerito0
Last seen 16 months ago

I am 8 years late but ran into the same problem and thought I'd leave something here for further Googlers:

Check your geneList vector and make sure it doesn't have any NA values in it! That was what was breaking it for me.

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