[BioC] GOstats and custom annotation problem
Dario Greco
dario.greco at helsinki.fi
Thu Jan 4 17:59:21 CET 2007
hi Sean,
as you advised, i have installed AnnBuilder 1.12.0 and re-built the
annotation package.
as a result, it seems that it keeps creating the "LOCUSID" object, as
shown by the QCDATA screen.
hgu133pEG800QCDATA
$name
[1] "hgu133pEG800"
$built
[1] "Created: Thu Jan 4 15:41:28 2007 "
$probeNum
[1] 17663
$numMissMatch
[1] "None"
$probeMissMatch
[1] "None"
$probeMapped
hgu133pEG800ACCNUM hgu133pEG800CHRLOC hgu133pEG800CHR
0 16128 17268
hgu133pEG800ENZYME hgu133pEG800GENENAME hgu133pEG800GO
1787 15757 14133
hgu133pEG800LOCUSID hgu133pEG800MAP hgu133pEG800OMIM
17601 17180 10240
hgu133pEG800PATH hgu133pEG800PMID hgu133pEG800REFSEQ
3756 16943 17177
hgu133pEG800SUMFUNC hgu133pEG800SYMBOL hgu133pEG800UNIGENE
0 17268 16998
$otherMapped
hgu133pEG800CHRLENGTHS hgu133pEG800ENZYME2PROBE
hgu133pEG800GO2ALLPROBES
25
778 7748
hgu133pEG800GO2PROBE hgu133pEG800ORGANISM
hgu133pEG800PATH2PROBE
5950
1 189
hgu133pEG800PFAM hgu133pEG800PMID2PROBE
hgu133pEG800PROSITE
13185
132527 9246
and 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.U
TF-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_ID
ENTIFICATION=C
attached base packages:
[1] "tools" "methods" "stats" "graphics" "grDevices" "utils"
[7] "datasets" "base"
other attached packages:
AnnBuilder RSQLite DBI annotate XML Biobase
"1.12.0" "0.4-1" "0.1-10" "1.12.0" "0.99-8" "1.12.2"
is this a compatibility issue between AnnBuilder and GOstats?
in BioC 1.8 everything worked fine, as GOstats was happy with
"xxxLOCUSID" objects.
any further suggestion?
thanks again,
d
--
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
Lab WebPage:
http://www.biocenter.helsinki.fi/bi/dna-microarray/
Personal WebPage:
http://www.biocenter.helsinki.fi/bi/dna-microarray/dario.htm
On Jan 4, 2007, at 2:08 PM, Sean Davis wrote:
> On Thursday 04 January 2007 06:56, Dario Greco wrote:
>> 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_U
>> S.UTF-
>> 8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-
>> 8;LC_NA
>> ME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTI
>> FICATIO
>> N=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"
>
> Is this an AnnBuilder version issue? It looks like the newest
> released
> version of AnnBuilder is 1.12.0, whereas your version is 1.11.6
> (and we don't
> know what version you used to actually create the annotation package).
>
> Sean
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