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

[Valerie Obenchain]

Hi Diwan,

1.18.4 is not the most current release version. You can see the build 
reports and most current versions here,

http://bioconductor.org/checkResults/release/bioc-LATEST/
http://bioconductor.org/checkResults/devel/bioc-LATEST/


The code below is working for me with both AnnotationDbi 1.20.7 
(release) and 1.21.16 (devel).


 > frame = toTable(org.Rn.egGO)
 > goframeData = data.frame(frame$go_id, frame$Evidence, frame$gene_id)
 > goFrame = GOFrame(goframeData, organism = "Rattus norvegicus")
Loading required package: GO.db
 > sessionInfo()
R version 2.15.2 RC (2012-10-24 r61009)
Platform: x86_64-unknown-linux-gnu (64-bit)

locale:
  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
  [3] 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
  [7] LC_PAPER=C                 LC_NAME=C
  [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
  [1] GO.db_2.8.0          GOstats_2.24.0       graph_1.36.2
  [4] Category_2.24.0      org.Rn.eg.db_2.8.1   RSQLite_0.11.2
  [7] DBI_0.2-5            AnnotationDbi_1.20.7 Biobase_2.18.0
[10] BiocGenerics_0.4.0   BiocInstaller_1.8.3

loaded via a namespace (and not attached):
  [1] annotate_1.36.0       AnnotationForge_1.0.3 genefilter_1.40.0
  [4] GSEABase_1.20.2       IRanges_1.16.6        parallel_2.15.2
  [7] RBGL_1.34.0           splines_2.15.2        stats4_2.15.2
[10] survival_2.37-4       tools_2.15.2          XML_3.95-0.1


Valerie


On 03/19/13 09:02, Diwan [guest] wrote:
>
> Hello,
> 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:
> 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
>
> --
> Sent via the guest posting facility at bioconductor.org.
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
>