[BioC] cateGOry error

[Oleg Sklyar]

> Based on a quick read of the code in Cateogry/R/cateGOryMatrix.R, it
> looks like these valus should be GO IDs (element of the categ argument
> to cateGOry).  Are you sure those values are not in go$go?
I did the grep and at least the 0024 does not appear there at all. By 
using %in% I find only 172. But I have further problems, like the 
following and starting to suspect that something is wrong with character 
operations:

 > class(entrez)
[1] "character"
 > entrez[120000:120010]
  [1] NA NA NA NA NA NA NA NA NA NA NA
 > which(is.na(entrez))
integer(0)
 > which(entrez=="NA")
integer(0)

How can I get onto those NA's?


 > sessionInfo()
R version 2.5.0 (2007-04-23)
x86_64-unknown-linux-gnu

locale:
LC_CTYPE=en_GB.UTF-8;LC_NUMERIC=C;LC_TIME=en_GB.UTF-8;LC_COLLATE=en_GB.UTF-8;LC_MONETARY=en_GB.UTF-8;LC_MESSAGES=en_GB.UTF-8;LC_PAPER=en_GB.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_GB.UTF-8;LC_IDENTIFICATION=C

attached base packages:
[1] "splines"   "tools"     "stats"     "graphics"  "grDevices" "utils"
[7] "datasets"  "methods"   "base"

other attached packages:
    Category      Matrix     lattice  genefilter    survival    annotate
     "2.2.1" "0.9975-11"    "0.15-4"    "1.14.1"      "2.31"    "1.14.1"
          GO        KEGG       graph     Biobase     biomaRt       RCurl
    "1.16.0"    "1.16.0"    "1.14.0"    "1.14.0"    "1.10.0"     "0.8-0"
         XML
     "1.9-0"