[Bioc-devel] error message in cateGOry function

[Florian Hahne]

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"