[BioC] GOstats and custom annotation problem

[Dario Greco]

dear list,
i am trying to run GOHyperG using a custom annotation package created with 
AnnBuilder.

the package is:
hgu133pEG800QCDATA
$name
[1] "hgu133pEG800"
$built
[1] "Created: Tue Oct 24 15:08:55 2006 "
$probeNum
[1] 17663
$numMissMatch
[1] "None"
$probeMissMatch
[1] "None"
$probeMapped
  hgu133pEG800ACCNUM   hgu133pEG800CHRLOC      hgu133pEG800CHR
                   0                16174                17275
  hgu133pEG800ENZYME hgu133pEG800GENENAME       hgu133pEG800GO
                1783                15693                13226
 hgu133pEG800LOCUSID      hgu133pEG800MAP     hgu133pEG800OMIM
               17601                17185                10116
    hgu133pEG800PATH     hgu133pEG800PMID   hgu133pEG800REFSEQ
                3744                16930                16312
 hgu133pEG800SUMFUNC   hgu133pEG800SYMBOL  hgu133pEG800UNIGENE
                   0                17275                17007
$otherMapped
  hgu133pEG800CHRLENGTHS hgu133pEG800ENZYME2PROBE hgu133pEG800GO2ALLPROBES
                      25                      777                     6612
    hgu133pEG800GO2PROBE     hgu133pEG800ORGANISM   hgu133pEG800PATH2PROBE
                    5090                        1                      187
        hgu133pEG800PFAM   hgu133pEG800PMID2PROBE      hgu133pEG800PROSITE
                   13171                   128579                     9223


when i run GOHyperG, i run into the following error:
GOHyperG(sample, lib="hgu133pEG800", what="CC")
Error in get(x, envir, mode, inherits) : variable "hgu133pEG800ENTREZID" of 
mode "environment" was not found

it seems that GOHyperG looks for an object like "mypkgENTREZID", while 
AnnBuilder creates an object named "mypkgLOCUSID".

do you have any suggestions for this problem?

here is my session info:
sessionInfo()
R version 2.4.0 Patched (2006-11-03 r39789)
i686-redhat-linux-gnu
locale:
LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C
attached base packages:
[1] "splines"   "tools"     "methods"   "stats"     "graphics"  "grDevices"
[7] "utils"     "datasets"  "base"
other attached packages:
hgu133pEG800      GOstats     Category   genefilter     survival         KEGG
     "1.0.0"      "2.0.4"      "2.0.3"     "1.12.0"       "2.29"     "1.10.0"
        RBGL        graph           GO   AnnBuilder      RSQLite          DBI
    "1.10.0"     "1.12.0"     "1.14.1"     "1.11.6"      "0.4-1"     "0.1-10"
    annotate          XML      Biobase
    "1.12.0"     "0.99-8"     "1.12.2"


thank you in advance for your help.
dario
-- 

Dario Greco

Institute of Biotechnology - University of Helsinki
Building Cultivator II
P.O.Box 56      Viikinkaari 4
FIN-00014       Finland

Office: +358 9 191 58951
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