Problem with geneAnswers, Reactome and some converted affy IDs
0
0
Entering edit mode
@ulrik-stervbo-1723
Last seen 5.6 years ago
Germany
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(org.Hs.eg.db) 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[!is.na(entrez.ids)] go.profile <- geneAnswersBuilder(entrez.ids, 'org.Hs.eg.db', 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 org.Hs.eg.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 • 514 views
ADD COMMENT

Login before adding your answer.

Traffic: 267 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6