[BioC] Error in .testGOFrame(x, organism)
Diwan [guest]
guest at bioconductor.org
Tue Mar 19 17:02:30 CET 2013
Hello,
I am trying to do GO enrichment analysis. When I use âGOFrameâ, I get the following error message:
> frame = toTable(org.Rn.egGO)
> goframeData = data.frame(frame$go_id, frame$Evidence, frame$gene_id)
> goFrame = GOFrame(goframeData, organism = "Rattus norvegicus")
Error in .testGOFrame(x, organism) :
All of the Evidence codes in your data.frame object must be legitimate Evidence Codes.
I checked the BioC mail list and noticed that same error was discussed before at:
https://stat.ethz.ch/pipermail/bioconductor/2012-May/045773.html
It was mentioned that a bug was fixed in AnnotationDbi version 1.18.1. I am using the most recent version AnnotationDbi version 1.18.4.
Could this be the source of error? Any help is greatly appreciated.
Thanks,
Diwan
-- output of sessionInfo():
> sessionInfo()
R version 2.15.2 (2012-10-26)
Platform: x86_64-redhat-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 LC_PAPER=C LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] rat2302cdf_2.10.0 KEGG.db_2.7.1 BiocInstaller_1.4.9 GSEABase_1.18.0 rat2302.db_2.7.1
[6] org.Rn.eg.db_2.7.1 annotate_1.34.1 GOstats_2.22.0 graph_1.34.0 Category_2.22.0
[11] GO.db_2.7.1 RSQLite_0.11.1 DBI_0.2-5 AnnotationDbi_1.18.4 Biobase_2.16.0
loaded via a namespace (and not attached):
[1] genefilter_1.38.0 IRanges_1.12.6 RBGL_1.30.1 splines_2.15.2 survival_2.37-4 tools_2.15.2
[7] XML_3.9-4 xtable_1.7-0
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