GOstats and custom annotation problem
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Dario Greco ▴ 310
@dario-greco-1536
Last seen 9.6 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
Annotation GO annotate genefilter graph AnnBuilder RBGL GOstats Category Annotation GO • 1.6k views
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@sean-davis-490
Last seen 3 months ago
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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_ US.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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hi, thanks for your reply. actually i have tried to build a new package with AnnBuilder 1.11.6 and it creates the "LOCUSID" object. i will try with 1.12.0. thanks d On Thursday 04 January 2007 14:08, 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=e n_US.UT > >F- > > 8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.U TF-8;LC > >_NA > > ME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDE NTIFICA > >TIO 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 -- 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
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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.UT F- 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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Hi, It would help if you could give the complete sequence of commands that you used. It is pretty hard for us to guess just what you did. I have just built a custom annotation package and don't see this behavior. My code looks like: ABPkgBuilder(baseName="eSet22.GB", baseMapType="gbNRef", pkgName="ISBOvarianAnnotation", pkgPath=".", organism="Homo sapiens", otherSrc=c( REFSEQ="eSet22.refseq", UG="eSet22.UG"), version="1.0.0", author=list( authors="Robert Gentleman", maintainer="R. Gentleman <rgentlem at="" fhcrc.org="">" ) ) so you would need to replace the baseName variable and the otherSrc variables (among other things) to what you are going to use. Also, after using Annbuilder did you build and install the package? Using new version numbers as you proceed helps to detect cases where things have not gone as expected. In any event, why not just go library("hgu133pEG800") hgu133pEG800ENTREZID <- hgu133pEG800LOCUSID and then things should be fine. best wishes Robert Dario Greco wrote: > 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;L C_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 > -- Robert Gentleman, PhD Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M2-B876 PO Box 19024 Seattle, Washington 98109-1024 206-667-7700 rgentlem at fhcrc.org
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Hi Robert, thanks for your post. these are the commands i have used in AnnBuilder: version<-"1.1.0" pkgPath<-getwd() mypkg <- function(pkgPath, version) {ABPkgBuilder(baseName="hgu133pEG800.txt",baseMapType="ll",pkgName="hg u133pEG800", pkgPath=pkgPath,organism="Homo sapiens",version=version,author=list(authors="Dario Greco",maintainer="Dario Greco <dario.greco at="" helsinki.fi="">"))} mypkg(pkgPath, version) after this, i have build and installed the package as root: R CMD build hgu133pEG800 R CMD INSTALL hgu133pEG800_1.1.0.tar.gz both these gave normal output. i will try now to re-assign LOCUSID to ENTREZID, as you suggested. i will report the output soon. thank you again, d On Thursday 04 January 2007 19:37, Robert Gentleman wrote: > Hi, > It would help if you could give the complete sequence of commands > that you used. It is pretty hard for us to guess just what you did. I > have just built a custom annotation package and don't see this behavior. > > My code looks like: > > ABPkgBuilder(baseName="eSet22.GB", > baseMapType="gbNRef", > pkgName="ISBOvarianAnnotation", > pkgPath=".", > organism="Homo sapiens", > otherSrc=c( REFSEQ="eSet22.refseq", UG="eSet22.UG"), > version="1.0.0", > author=list( > authors="Robert Gentleman", > maintainer="R. Gentleman <rgentlem at="" fhcrc.org="">" > ) > ) > > so you would need to replace the baseName variable and the otherSrc > variables (among other things) to what you are going to use. > > Also, after using Annbuilder did you build and install the package? > Using new version numbers as you proceed helps to detect cases where > things have not gone as expected. > > > In any event, why not just go > library("hgu133pEG800") > hgu133pEG800ENTREZID <- hgu133pEG800LOCUSID > > and then things should be fine. > > > > best wishes > Robert > > Dario Greco wrote: > > 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=e n_US.U > > TF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_U S.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
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hi again, Robert's suggestion library("hgu133pEG800") hgu133pEG800ENTREZID <- hgu133pEG800LOCUSID worked fine (of course). so at the moment, i would say that this is fixed, unless someone doesn't want to make AnnBuilder and GOstats fully compatible (maybe useful option anyway)... :) thank you for your kind help. 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 7:37 PM, Robert Gentleman wrote: > Hi, > It would help if you could give the complete sequence of commands > that you used. It is pretty hard for us to guess just what you > did. I have just built a custom annotation package and don't see > this behavior. > > My code looks like: > > ABPkgBuilder(baseName="eSet22.GB", > baseMapType="gbNRef", > pkgName="ISBOvarianAnnotation", > pkgPath=".", > organism="Homo sapiens", > otherSrc=c( REFSEQ="eSet22.refseq", UG="eSet22.UG"), > version="1.0.0", > author=list( > authors="Robert Gentleman", > maintainer="R. Gentleman <rgentlem at="" fhcrc.org="">" > ) > ) > > so you would need to replace the baseName variable and the otherSrc > variables (among other things) to what you are going to use. > > Also, after using Annbuilder did you build and install the package? > Using new version numbers as you proceed helps to detect cases > where things have not gone as expected. > > > In any event, why not just go > library("hgu133pEG800") > hgu133pEG800ENTREZID <- hgu133pEG800LOCUSID > > and then things should be fine. > > > > best wishes > Robert > > > Dario Greco wrote: >> 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_U >> S.U >> TF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.U >> TF- >> 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 > > -- > Robert Gentleman, PhD > Program in Computational Biology > Division of Public Health Sciences > Fred Hutchinson Cancer Research Center > 1100 Fairview Ave. N, M2-B876 > PO Box 19024 > Seattle, Washington 98109-1024 > 206-667-7700 > rgentlem at fhcrc.org
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