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

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