Problem with geneAnswers, Reactome and some converted affy IDs
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Last seen 6.4 years ago
Hello everyone, When I run the code below, the geneAnswersReadable() fails because vector lengths do not match (the function actually failing is getCategoryTerms()). Can anyone repeat this? The funny bit is, that - as far as I can see - getCategoryTerms() should return what it got, when the catType is reactome.path. It will work with a subset of the affys, and the failure is unrelated to the one-to-many conversion warning thrown by AnnotationDbi::select(). The offending affys are c("219759_at", "226481_at", "227462_at", "235104_at"), converted to c("64167", "9730", "64167", "64167"). Cheers, Ulrik Minimal example: library(GeneAnswers) library( library(hgu133plus2.db) probe.ids <-c("1553269_at", "1568983_a_at", "203628_at", "204418_x_at", "204950_at", "209081_s_at", "209442_x_at", "213005_s_at", "213534_s_at", "213645_at", "214246_x_at", "215606_s_at", "216945_x_at", "217787_s_at", "217788_s_at", "218231_at", "218754_at", "219315_s_at", "219627_at", "219759_at", "219871_at", "220349_s_at", "221728_x_at", "223528_s_at", "223583_at", "224588_at", "225758_s_at", "225794_s_at", "225795_at", "225904_at", "226444_at", "226481_at", "226693_at", "227259_at", "227462_at", "227474_at", "227984_at", "229497_at", "229748_x_at", "230323_s_at", "231013_at", "231979_at", "235104_at", "235172_at", "235274_at") entrez.ids <- AnnotationDbi::select(hgu133plus2.db, probe.ids, "ENTREZID", "PROBEID") entrez.ids <- entrez.ids$ENTREZID entrez.ids <- entrez.ids[!] go.profile <- geneAnswersBuilder(entrez.ids, '', categoryType='reactome.path', testType='h', pvalueT=0.1, FDR.correct=TRUE) go.res <- geneAnswersReadable(go.profile) > sessionInfo() R version 3.0.3 (2014-03-06) Platform: i386-w64-mingw32/i386 (32-bit) locale: [1] LC_COLLATE=German_Germany.1252 LC_CTYPE=German_Germany.1252 LC_MONETARY=German_Germany.1252 [4] LC_NUMERIC=C LC_TIME=German_Germany.1252 attached base packages: [1] parallel stats graphics grDevices utils datasets methods base other attached packages: [1] reactome.db_1.46.1 hgu133plus2.db_2.10.1 GeneAnswers_2.4.0 RColorBrewer_1.0-5 [6] Heatplus_2.8.0 MASS_7.3-30 RSQLite_0.11.4 DBI_0.2-7 XML_3.98-1.1 [11] annotate_1.40.1 AnnotationDbi_1.24.0 Biobase_2.22.0 BiocGenerics_0.8.0 RCurl_1.95-4.1 [16] bitops_1.0-6 igraph_0.7.0 loaded via a namespace (and not attached): [1] graph_1.40.1 IRanges_1.20.7 RBGL_1.38.0 stats4_3.0.3 tools_3.0.3 xtable_1.7-3 [[alternative HTML version deleted]]
hgu133plus2 probe hgu133plus2 probe • 559 views

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