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Dario Greco
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310
@dario-greco-1536
Last seen 10.2 years ago
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
Fax: +358 9 191 58952
Mobile: +358 44 023 5780