[Bioc-devel] error message in cateGOry function

[Wolfgang Huber]

Hi Florian,

this was a bug and I recently fixed it. Please try a more recent version 
of the package, this will do exactly what you want.

  Best wishes
  Wolfgang


> Hi all,
> I frequently use the Category package for geneset enrichment based on GO 
> terms. My GO annotation information often comes from biomaRt or other 
> sources and not directly from the GO package, so now and then I run into 
> version conflicts when a given GO term is not or no longer included in 
> the GO package. The cateGOry function used to stop with an error message 
> listing the unknown GO terms, but in one of the later versions this 
> changed to a list of indices into the vector of GO terms. Now the 
> problem is that these indices do not match the originial imput vector 
> (some remodeling goes on in the augmentByAncestorsSmart function, I 
> think. So in order to identify the missing GO terms I have to debug and 
> dig deep into the guts of augmentByAncestors. Wouldn't it be possible to 
> report the missing GO terms via the GO identifier (as it was before) so 
> I can easily remove them from my analysis. Or should this be done by the 
> function with a warning?
> Cheers,
> Florian
> 
>  > sessionInfo()
> R version 2.5.0 Under development (unstable) (2007-01-24 r40564)
> i686-pc-linux-gnu
> 
> locale:
> LC_CTYPE=en_US;LC_NUMERIC=C;LC_TIME=en_US;LC_COLLATE=en_US;LC_MONETARY=en_US;LC_MESSAGES=en_US;LC_PAPER=en_US;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US;LC_IDENTIFICATION=C
> 
> attached base packages:
>  [1] "splines"   "grid"      "tools"     "stats"     "graphics"  "grDevices"
>  [7] "datasets"  "utils"     "methods"   "base"    
> 
> other attached packages:
>      GOstats         RBGL      biomaRt        RCurl          XML    
> rnaiUtils
>      "2.2.1"     "1.11.4"     "1.10.0"      "0.8-0"      "1.4-1"        
> "1.0"
>     Category       Matrix      lattice     annotate           GO         
> KEGG
>      "2.2.2"  "0.9975-11"    "0.14-16"     "1.14.1"     "1.16.0"    
> "1.15.12"
>        graph      cellHTS   genefilter     survival        prada 
> RColorBrewer
>     "1.14.0"      "1.5.9"     "1.13.8"       "2.30"     "1.12.0"      
> "0.2-3"
>      Biobase
>    "1.13.39"
> 
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