[BioC] Error in .testGOFrame(x, organism)

Diwan [guest] guest at bioconductor.org
Tue Mar 19 17:02:30 CET 2013

I am trying to do GO enrichment analysis. When I use “GOFrame”, 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:
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.

 -- output of sessionInfo(): 

> sessionInfo()
R version 2.15.2 (2012-10-26)
Platform: x86_64-redhat-linux-gnu (64-bit)

 [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                 

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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