Question: problem with Category package and custom annotationDbi
0
gravatar for Mark W Kimpel
11.0 years ago by
Mark W Kimpel830
Mark W Kimpel830 wrote:
Today I believe I successfuly built a annotation package for my Affy Rat Gene ST data using annotationDbi, at least I got no errors during the build and it loads properly. I get the following error output, however, when I try to run hyperGTest, package Category, on a vector of Entrez Gene IDs and a vector of the gene universe of the chip. I suspect I did something wrong when building the annotation package, but I have no clue what that could be. I've used this same code with chipsets whose annotation packages are built by the BioConductor team without issue. > params <- new("GOHyperGParams", geneIds = myEGs, + universeGeneIds = myGeneUniverse, + annotation = annotation(AOP$eSet), + ontology = "BP", pvalueCutoff = 0.05, conditional = TRUE, testDirection = "over") > params A GOHyperGParams instance category: GO annotation: ragene10stv1 > hyperGTest(params) Error in getUniverseHelper(probes, datPkg, entrezIds) : No Entrez Gene ids left in universe Enter a frame number, or 0 to exit 1: hyperGTest(params) 2: .valueClassTest(standardGeneric("hyperGTest"), "HyperGResultBase", "hyperGT 3: is(object, Cl) 4: is(object, Cl) 5: universeBuilder(p) 6: universeBuilder(p) 7: getUniverseViaGo(p) 8: getUniverseHelper(probes, datPkg, entrezIds) Selection: 8 Called from: eval(expr, envir, enclos) Browse[1]> ls() [1] "datPkg" "entrezIds" "probes" "univ" Browse[1]> datPkg An object of class "ArabadopsisDatPkg" Slot "name": [1] "ragene10stv1" Browse[1]> entrezIds[1:5] [1] "65049" "60444" "313914" "140941" "306868" Browse[1]> probes[1:5] [1] "10701636" "10701643" "10701654" "10701663" "10701679" Browse[1]> univ character(0) Browse[1]> ------------------------------------------------------------ Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry Indiana University School of Medicine 15032 Hunter Court, Westfield, IN 46074 (317) 490-5129 Work, & Mobile & VoiceMail (317) 399-1219 Home Skype: mkimpel "The real problem is not whether machines think but whether men do." -- B. F. Skinner
ADD COMMENTlink modified 11.0 years ago by rgentleman5.5k • written 11.0 years ago by Mark W Kimpel830
Answer: problem with Category package and custom annotationDbi
0
gravatar for Marc Carlson
11.0 years ago by
Marc Carlson7.2k
United States
Marc Carlson7.2k wrote:
Hi Mark, If the package you built and installed were called "MarkPackage.db", then what would be the output of "MarkPackage()" (right after you loaded it)? Also, what is the output of sessionInfo()? Marc Mark Kimpel wrote: > Today I believe I successfuly built a annotation package for my Affy > Rat Gene ST data using annotationDbi, at least I got no errors during > the build and it loads properly. I get the following error output, > however, when I try to run hyperGTest, package Category, on a vector > of Entrez Gene IDs and a vector of the gene universe of the chip. I > suspect I did something wrong when building the annotation package, > but I have no clue what that could be. I've used this same code with > chipsets whose annotation packages are built by the BioConductor team > without issue. > > >> params <- new("GOHyperGParams", geneIds = myEGs, >> > + universeGeneIds = myGeneUniverse, > + annotation = annotation(AOP$eSet), > + ontology = "BP", pvalueCutoff = 0.05, conditional > = TRUE, testDirection = "over") > >> params >> > A GOHyperGParams instance > category: GO > annotation: ragene10stv1 > >> hyperGTest(params) >> > Error in getUniverseHelper(probes, datPkg, entrezIds) : > No Entrez Gene ids left in universe > > Enter a frame number, or 0 to exit > > 1: hyperGTest(params) > 2: .valueClassTest(standardGeneric("hyperGTest"), "HyperGResultBase", "hyperGT > 3: is(object, Cl) > 4: is(object, Cl) > 5: universeBuilder(p) > 6: universeBuilder(p) > 7: getUniverseViaGo(p) > 8: getUniverseHelper(probes, datPkg, entrezIds) > > Selection: 8 > Called from: eval(expr, envir, enclos) > Browse[1]> ls() > [1] "datPkg" "entrezIds" "probes" "univ" > Browse[1]> datPkg > An object of class "ArabadopsisDatPkg" > Slot "name": > [1] "ragene10stv1" > > Browse[1]> entrezIds[1:5] > [1] "65049" "60444" "313914" "140941" "306868" > Browse[1]> probes[1:5] > [1] "10701636" "10701643" "10701654" "10701663" "10701679" > Browse[1]> univ > character(0) > Browse[1]> > > ------------------------------------------------------------ > Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry > Indiana University School of Medicine > > 15032 Hunter Court, Westfield, IN 46074 > > (317) 490-5129 Work, & Mobile & VoiceMail > (317) 399-1219 Home > Skype: mkimpel > > "The real problem is not whether machines think but whether men do." > -- B. F. Skinner > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > >
ADD COMMENTlink written 11.0 years ago by Marc Carlson7.2k
> ragene10stv1() Quality control information for ragene10stv1: This package has the following mappings: ragene10stv1ACCNUM has 0 mapped keys (of 29214 keys) ragene10stv1ALIAS2PROBE has 31410 mapped keys (of 31410 keys) ragene10stv1CHR has 20998 mapped keys (of 29214 keys) ragene10stv1CHRLENGTHS has 23 mapped keys (of 23 keys) ragene10stv1CHRLOC has 13092 mapped keys (of 29214 keys) ragene10stv1CHRLOCEND has 13092 mapped keys (of 29214 keys) ragene10stv1ENSEMBL has 15812 mapped keys (of 29214 keys) ragene10stv1ENSEMBL2PROBE has 14570 mapped keys (of 14570 keys) ragene10stv1ENTREZID has 21170 mapped keys (of 29214 keys) ragene10stv1ENZYME has 1586 mapped keys (of 29214 keys) ragene10stv1ENZYME2PROBE has 705 mapped keys (of 705 keys) ragene10stv1GENENAME has 21170 mapped keys (of 29214 keys) ragene10stv1GO has 13813 mapped keys (of 29214 keys) ragene10stv1GO2ALLPROBES has 9850 mapped keys (of 9850 keys) ragene10stv1GO2PROBE has 7430 mapped keys (of 7430 keys) ragene10stv1MAP has 20351 mapped keys (of 29214 keys) ragene10stv1PATH has 4357 mapped keys (of 29214 keys) ragene10stv1PATH2PROBE has 206 mapped keys (of 206 keys) ragene10stv1PFAM has 17187 mapped keys (of 29214 keys) ragene10stv1PMID has 12198 mapped keys (of 29214 keys) ragene10stv1PMID2PROBE has 36641 mapped keys (of 36641 keys) ragene10stv1PROSITE has 17187 mapped keys (of 29214 keys) ragene10stv1REFSEQ has 18683 mapped keys (of 29214 keys) ragene10stv1SYMBOL has 21170 mapped keys (of 29214 keys) ragene10stv1UNIGENE has 17585 mapped keys (of 29214 keys) ragene10stv1UNIPROT has 9826 mapped keys (of 29214 keys) Additional Information about this package: DB schema: RATCHIP_DB DB schema version: 1.0 Organism: Rattus norvegicus Date for NCBI data: 2008-Sep2 Date for GO data: 200808 Date for KEGG data: 2008-Sep2 Date for Golden Path data: 2006-Jun20 Date for IPI data: 2008-Sep02 Date for Ensembl data: 2008-Jul23 > sessionInfo() R version 2.8.0 (2008-10-20) x86_64-unknown-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=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_N AME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTI FICATION=C attached base packages: [1] tools stats graphics grDevices utils datasets methods [8] base other attached packages: [1] ragene10stv1.db_1.0.0 RSQLite_0.7-0 DBI_0.2-4 [4] AnnotationDbi_1.4.0 Biobase_2.2.0 graph_1.20.0 loaded via a namespace (and not attached): [1] cluster_1.11.11 > ------------------------------------------------------------ Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry Indiana University School of Medicine 15032 Hunter Court, Westfield, IN 46074 (317) 490-5129 Work, & Mobile & VoiceMail (317) 399-1219 Home Skype: mkimpel "The real problem is not whether machines think but whether men do." -- B. F. Skinner ****************************************************************** On Wed, Oct 22, 2008 at 7:41 PM, Marc Carlson <mcarlson at="" fhcrc.org=""> wrote: > Hi Mark, > > If the package you built and installed were called "MarkPackage.db", > then what would be the output of "MarkPackage()" (right after you loaded > it)? Also, what is the output of sessionInfo()? > > Marc > > > > > Mark Kimpel wrote: >> Today I believe I successfuly built a annotation package for my Affy >> Rat Gene ST data using annotationDbi, at least I got no errors during >> the build and it loads properly. I get the following error output, >> however, when I try to run hyperGTest, package Category, on a vector >> of Entrez Gene IDs and a vector of the gene universe of the chip. I >> suspect I did something wrong when building the annotation package, >> but I have no clue what that could be. I've used this same code with >> chipsets whose annotation packages are built by the BioConductor team >> without issue. >> >> >>> params <- new("GOHyperGParams", geneIds = myEGs, >>> >> + universeGeneIds = myGeneUniverse, >> + annotation = annotation(AOP$eSet), >> + ontology = "BP", pvalueCutoff = 0.05, conditional >> = TRUE, testDirection = "over") >> >>> params >>> >> A GOHyperGParams instance >> category: GO >> annotation: ragene10stv1 >> >>> hyperGTest(params) >>> >> Error in getUniverseHelper(probes, datPkg, entrezIds) : >> No Entrez Gene ids left in universe >> >> Enter a frame number, or 0 to exit >> >> 1: hyperGTest(params) >> 2: .valueClassTest(standardGeneric("hyperGTest"), "HyperGResultBase", "hyperGT >> 3: is(object, Cl) >> 4: is(object, Cl) >> 5: universeBuilder(p) >> 6: universeBuilder(p) >> 7: getUniverseViaGo(p) >> 8: getUniverseHelper(probes, datPkg, entrezIds) >> >> Selection: 8 >> Called from: eval(expr, envir, enclos) >> Browse[1]> ls() >> [1] "datPkg" "entrezIds" "probes" "univ" >> Browse[1]> datPkg >> An object of class "ArabadopsisDatPkg" >> Slot "name": >> [1] "ragene10stv1" >> >> Browse[1]> entrezIds[1:5] >> [1] "65049" "60444" "313914" "140941" "306868" >> Browse[1]> probes[1:5] >> [1] "10701636" "10701643" "10701654" "10701663" "10701679" >> Browse[1]> univ >> character(0) >> Browse[1]> >> >> ------------------------------------------------------------ >> Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry >> Indiana University School of Medicine >> >> 15032 Hunter Court, Westfield, IN 46074 >> >> (317) 490-5129 Work, & Mobile & VoiceMail >> (317) 399-1219 Home >> Skype: mkimpel >> >> "The real problem is not whether machines think but whether men do." >> -- B. F. Skinner >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >> >> > >
ADD REPLYlink written 11.0 years ago by Mark W Kimpel830
Hi Mark, >From that output it looks like your package was made successfully. I suspect that if you show us an example of what you were doing that we might find the trouble in there. Marc Mark Kimpel wrote: >> ragene10stv1() >> > Quality control information for ragene10stv1: > > > This package has the following mappings: > > ragene10stv1ACCNUM has 0 mapped keys (of 29214 keys) > ragene10stv1ALIAS2PROBE has 31410 mapped keys (of 31410 keys) > ragene10stv1CHR has 20998 mapped keys (of 29214 keys) > ragene10stv1CHRLENGTHS has 23 mapped keys (of 23 keys) > ragene10stv1CHRLOC has 13092 mapped keys (of 29214 keys) > ragene10stv1CHRLOCEND has 13092 mapped keys (of 29214 keys) > ragene10stv1ENSEMBL has 15812 mapped keys (of 29214 keys) > ragene10stv1ENSEMBL2PROBE has 14570 mapped keys (of 14570 keys) > ragene10stv1ENTREZID has 21170 mapped keys (of 29214 keys) > ragene10stv1ENZYME has 1586 mapped keys (of 29214 keys) > ragene10stv1ENZYME2PROBE has 705 mapped keys (of 705 keys) > ragene10stv1GENENAME has 21170 mapped keys (of 29214 keys) > ragene10stv1GO has 13813 mapped keys (of 29214 keys) > ragene10stv1GO2ALLPROBES has 9850 mapped keys (of 9850 keys) > ragene10stv1GO2PROBE has 7430 mapped keys (of 7430 keys) > ragene10stv1MAP has 20351 mapped keys (of 29214 keys) > ragene10stv1PATH has 4357 mapped keys (of 29214 keys) > ragene10stv1PATH2PROBE has 206 mapped keys (of 206 keys) > ragene10stv1PFAM has 17187 mapped keys (of 29214 keys) > ragene10stv1PMID has 12198 mapped keys (of 29214 keys) > ragene10stv1PMID2PROBE has 36641 mapped keys (of 36641 keys) > ragene10stv1PROSITE has 17187 mapped keys (of 29214 keys) > ragene10stv1REFSEQ has 18683 mapped keys (of 29214 keys) > ragene10stv1SYMBOL has 21170 mapped keys (of 29214 keys) > ragene10stv1UNIGENE has 17585 mapped keys (of 29214 keys) > ragene10stv1UNIPROT has 9826 mapped keys (of 29214 keys) > > > Additional Information about this package: > > DB schema: RATCHIP_DB > DB schema version: 1.0 > Organism: Rattus norvegicus > Date for NCBI data: 2008-Sep2 > Date for GO data: 200808 > Date for KEGG data: 2008-Sep2 > Date for Golden Path data: 2006-Jun20 > Date for IPI data: 2008-Sep02 > Date for Ensembl data: 2008-Jul23 > >> sessionInfo() >> > R version 2.8.0 (2008-10-20) > x86_64-unknown-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=C;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_IDEN TIFICATION=C > > attached base packages: > [1] tools stats graphics grDevices utils datasets methods > [8] base > > other attached packages: > [1] ragene10stv1.db_1.0.0 RSQLite_0.7-0 DBI_0.2-4 > [4] AnnotationDbi_1.4.0 Biobase_2.2.0 graph_1.20.0 > > loaded via a namespace (and not attached): > [1] cluster_1.11.11 > > ------------------------------------------------------------ > Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry > Indiana University School of Medicine > > 15032 Hunter Court, Westfield, IN 46074 > > (317) 490-5129 Work, & Mobile & VoiceMail > (317) 399-1219 Home > Skype: mkimpel > > "The real problem is not whether machines think but whether men do." > -- B. F. Skinner > ****************************************************************** > > > > On Wed, Oct 22, 2008 at 7:41 PM, Marc Carlson <mcarlson at="" fhcrc.org=""> wrote: > >> Hi Mark, >> >> If the package you built and installed were called "MarkPackage.db", >> then what would be the output of "MarkPackage()" (right after you loaded >> it)? Also, what is the output of sessionInfo()? >> >> Marc >> >> >> >> >> Mark Kimpel wrote: >> >>> Today I believe I successfuly built a annotation package for my Affy >>> Rat Gene ST data using annotationDbi, at least I got no errors during >>> the build and it loads properly. I get the following error output, >>> however, when I try to run hyperGTest, package Category, on a vector >>> of Entrez Gene IDs and a vector of the gene universe of the chip. I >>> suspect I did something wrong when building the annotation package, >>> but I have no clue what that could be. I've used this same code with >>> chipsets whose annotation packages are built by the BioConductor team >>> without issue. >>> >>> >>> >>>> params <- new("GOHyperGParams", geneIds = myEGs, >>>> >>>> >>> + universeGeneIds = myGeneUniverse, >>> + annotation = annotation(AOP$eSet), >>> + ontology = "BP", pvalueCutoff = 0.05, conditional >>> = TRUE, testDirection = "over") >>> >>> >>>> params >>>> >>>> >>> A GOHyperGParams instance >>> category: GO >>> annotation: ragene10stv1 >>> >>> >>>> hyperGTest(params) >>>> >>>> >>> Error in getUniverseHelper(probes, datPkg, entrezIds) : >>> No Entrez Gene ids left in universe >>> >>> Enter a frame number, or 0 to exit >>> >>> 1: hyperGTest(params) >>> 2: .valueClassTest(standardGeneric("hyperGTest"), "HyperGResultBase", "hyperGT >>> 3: is(object, Cl) >>> 4: is(object, Cl) >>> 5: universeBuilder(p) >>> 6: universeBuilder(p) >>> 7: getUniverseViaGo(p) >>> 8: getUniverseHelper(probes, datPkg, entrezIds) >>> >>> Selection: 8 >>> Called from: eval(expr, envir, enclos) >>> Browse[1]> ls() >>> [1] "datPkg" "entrezIds" "probes" "univ" >>> Browse[1]> datPkg >>> An object of class "ArabadopsisDatPkg" >>> Slot "name": >>> [1] "ragene10stv1" >>> >>> Browse[1]> entrezIds[1:5] >>> [1] "65049" "60444" "313914" "140941" "306868" >>> Browse[1]> probes[1:5] >>> [1] "10701636" "10701643" "10701654" "10701663" "10701679" >>> Browse[1]> univ >>> character(0) >>> Browse[1]> >>> >>> ------------------------------------------------------------ >>> Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry >>> Indiana University School of Medicine >>> >>> 15032 Hunter Court, Westfield, IN 46074 >>> >>> (317) 490-5129 Work, & Mobile & VoiceMail >>> (317) 399-1219 Home >>> Skype: mkimpel >>> >>> "The real problem is not whether machines think but whether men do." >>> -- B. F. Skinner >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor at stat.math.ethz.ch >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >>> >>> >>> >> > >
ADD REPLYlink written 11.0 years ago by Marc Carlson7.2k
myEGs has length of 400 and all are in MyGeneUniverse, checked with setdiff. at hospital with mother having surgery today, so will post reproducible example when I can. assume that myEGs should be lengthy, not sure how to post this, hence the reason I did not post already. suggestions? thanks Mark ------------------------------------------------------------ Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry Indiana University School of Medicine 15032 Hunter Court, Westfield, IN 46074 (317) 490-5129 Work, & Mobile & VoiceMail (317) 399-1219 Home Skype: mkimpel "The real problem is not whether machines think but whether men do." -- B. F. Skinner ****************************************************************** On Thu, Oct 23, 2008 at 12:52 PM, Marc Carlson <mcarlson at="" fhcrc.org=""> wrote: > Hi Mark, > > From that output it looks like your package was made successfully. I > suspect that if you show us an example of what you were doing that we > might find the trouble in there. > > Marc > > > > > Mark Kimpel wrote: >>> ragene10stv1() >>> >> Quality control information for ragene10stv1: >> >> >> This package has the following mappings: >> >> ragene10stv1ACCNUM has 0 mapped keys (of 29214 keys) >> ragene10stv1ALIAS2PROBE has 31410 mapped keys (of 31410 keys) >> ragene10stv1CHR has 20998 mapped keys (of 29214 keys) >> ragene10stv1CHRLENGTHS has 23 mapped keys (of 23 keys) >> ragene10stv1CHRLOC has 13092 mapped keys (of 29214 keys) >> ragene10stv1CHRLOCEND has 13092 mapped keys (of 29214 keys) >> ragene10stv1ENSEMBL has 15812 mapped keys (of 29214 keys) >> ragene10stv1ENSEMBL2PROBE has 14570 mapped keys (of 14570 keys) >> ragene10stv1ENTREZID has 21170 mapped keys (of 29214 keys) >> ragene10stv1ENZYME has 1586 mapped keys (of 29214 keys) >> ragene10stv1ENZYME2PROBE has 705 mapped keys (of 705 keys) >> ragene10stv1GENENAME has 21170 mapped keys (of 29214 keys) >> ragene10stv1GO has 13813 mapped keys (of 29214 keys) >> ragene10stv1GO2ALLPROBES has 9850 mapped keys (of 9850 keys) >> ragene10stv1GO2PROBE has 7430 mapped keys (of 7430 keys) >> ragene10stv1MAP has 20351 mapped keys (of 29214 keys) >> ragene10stv1PATH has 4357 mapped keys (of 29214 keys) >> ragene10stv1PATH2PROBE has 206 mapped keys (of 206 keys) >> ragene10stv1PFAM has 17187 mapped keys (of 29214 keys) >> ragene10stv1PMID has 12198 mapped keys (of 29214 keys) >> ragene10stv1PMID2PROBE has 36641 mapped keys (of 36641 keys) >> ragene10stv1PROSITE has 17187 mapped keys (of 29214 keys) >> ragene10stv1REFSEQ has 18683 mapped keys (of 29214 keys) >> ragene10stv1SYMBOL has 21170 mapped keys (of 29214 keys) >> ragene10stv1UNIGENE has 17585 mapped keys (of 29214 keys) >> ragene10stv1UNIPROT has 9826 mapped keys (of 29214 keys) >> >> >> Additional Information about this package: >> >> DB schema: RATCHIP_DB >> DB schema version: 1.0 >> Organism: Rattus norvegicus >> Date for NCBI data: 2008-Sep2 >> Date for GO data: 200808 >> Date for KEGG data: 2008-Sep2 >> Date for Golden Path data: 2006-Jun20 >> Date for IPI data: 2008-Sep02 >> Date for Ensembl data: 2008-Jul23 >> >>> sessionInfo() >>> >> R version 2.8.0 (2008-10-20) >> x86_64-unknown-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=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;L C_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDE NTIFICATION=C >> >> attached base packages: >> [1] tools stats graphics grDevices utils datasets methods >> [8] base >> >> other attached packages: >> [1] ragene10stv1.db_1.0.0 RSQLite_0.7-0 DBI_0.2-4 >> [4] AnnotationDbi_1.4.0 Biobase_2.2.0 graph_1.20.0 >> >> loaded via a namespace (and not attached): >> [1] cluster_1.11.11 >> >> ------------------------------------------------------------ >> Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry >> Indiana University School of Medicine >> >> 15032 Hunter Court, Westfield, IN 46074 >> >> (317) 490-5129 Work, & Mobile & VoiceMail >> (317) 399-1219 Home >> Skype: mkimpel >> >> "The real problem is not whether machines think but whether men do." >> -- B. F. Skinner >> ****************************************************************** >> >> >> >> On Wed, Oct 22, 2008 at 7:41 PM, Marc Carlson <mcarlson at="" fhcrc.org=""> wrote: >> >>> Hi Mark, >>> >>> If the package you built and installed were called "MarkPackage.db", >>> then what would be the output of "MarkPackage()" (right after you loaded >>> it)? Also, what is the output of sessionInfo()? >>> >>> Marc >>> >>> >>> >>> >>> Mark Kimpel wrote: >>> >>>> Today I believe I successfuly built a annotation package for my Affy >>>> Rat Gene ST data using annotationDbi, at least I got no errors during >>>> the build and it loads properly. I get the following error output, >>>> however, when I try to run hyperGTest, package Category, on a vector >>>> of Entrez Gene IDs and a vector of the gene universe of the chip. I >>>> suspect I did something wrong when building the annotation package, >>>> but I have no clue what that could be. I've used this same code with >>>> chipsets whose annotation packages are built by the BioConductor team >>>> without issue. >>>> >>>> >>>> >>>>> params <- new("GOHyperGParams", geneIds = myEGs, >>>>> >>>>> >>>> + universeGeneIds = myGeneUniverse, >>>> + annotation = annotation(AOP$eSet), >>>> + ontology = "BP", pvalueCutoff = 0.05, conditional >>>> = TRUE, testDirection = "over") >>>> >>>> >>>>> params >>>>> >>>>> >>>> A GOHyperGParams instance >>>> category: GO >>>> annotation: ragene10stv1 >>>> >>>> >>>>> hyperGTest(params) >>>>> >>>>> >>>> Error in getUniverseHelper(probes, datPkg, entrezIds) : >>>> No Entrez Gene ids left in universe >>>> >>>> Enter a frame number, or 0 to exit >>>> >>>> 1: hyperGTest(params) >>>> 2: .valueClassTest(standardGeneric("hyperGTest"), "HyperGResultBase", "hyperGT >>>> 3: is(object, Cl) >>>> 4: is(object, Cl) >>>> 5: universeBuilder(p) >>>> 6: universeBuilder(p) >>>> 7: getUniverseViaGo(p) >>>> 8: getUniverseHelper(probes, datPkg, entrezIds) >>>> >>>> Selection: 8 >>>> Called from: eval(expr, envir, enclos) >>>> Browse[1]> ls() >>>> [1] "datPkg" "entrezIds" "probes" "univ" >>>> Browse[1]> datPkg >>>> An object of class "ArabadopsisDatPkg" >>>> Slot "name": >>>> [1] "ragene10stv1" >>>> >>>> Browse[1]> entrezIds[1:5] >>>> [1] "65049" "60444" "313914" "140941" "306868" >>>> Browse[1]> probes[1:5] >>>> [1] "10701636" "10701643" "10701654" "10701663" "10701679" >>>> Browse[1]> univ >>>> character(0) >>>> Browse[1]> >>>> >>>> ------------------------------------------------------------ >>>> Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry >>>> Indiana University School of Medicine >>>> >>>> 15032 Hunter Court, Westfield, IN 46074 >>>> >>>> (317) 490-5129 Work, & Mobile & VoiceMail >>>> (317) 399-1219 Home >>>> Skype: mkimpel >>>> >>>> "The real problem is not whether machines think but whether men do." >>>> -- B. F. Skinner >>>> >>>> _______________________________________________ >>>> Bioconductor mailing list >>>> Bioconductor at stat.math.ethz.ch >>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >>>> >>>> >>>> >>> >> >> > >
ADD REPLYlink written 11.0 years ago by Mark W Kimpel830
Answer: problem with Category package and custom annotationDbi
0
gravatar for rgentleman
11.0 years ago by
rgentleman5.5k
United States
rgentleman5.5k wrote:
Hi Mark, Please, you have posted often enough here and on the R list to know to follow the posting guide. You will need to post a reproducible example as well as the things that you already provided (like sessionInfo) and you should not really need us to be asking you to do that, at this point. In my experience, spending the few minutes it takes to create a reproducible example for others to use is sufficient to help you find the error. My guess is that either your list of EG ids (myEGs) is very short, and hence has no matches in the universe (also I have no idea what the universe is: myGeneUniverse) and perhaps there is no overlap, or the universe is remarkably small - in which case you would certainly get this answer. In this case the error is not likely to be with how you constructed the package do note (from your later email) ragene10stv1GO has 13813 mapped keys (of 29214 keys) so only about 47% of your keys have any GO annotation - again, you could easily check to see if the genes in myEGs have annotations. best wishes Robert Mark Kimpel wrote: > Today I believe I successfuly built a annotation package for my Affy > Rat Gene ST data using annotationDbi, at least I got no errors during > the build and it loads properly. I get the following error output, > however, when I try to run hyperGTest, package Category, on a vector > of Entrez Gene IDs and a vector of the gene universe of the chip. I > suspect I did something wrong when building the annotation package, > but I have no clue what that could be. I've used this same code with > chipsets whose annotation packages are built by the BioConductor team > without issue. > >> params <- new("GOHyperGParams", geneIds = myEGs, > + universeGeneIds = myGeneUniverse, > + annotation = annotation(AOP$eSet), > + ontology = "BP", pvalueCutoff = 0.05, conditional > = TRUE, testDirection = "over") >> params > A GOHyperGParams instance > category: GO > annotation: ragene10stv1 >> hyperGTest(params) > Error in getUniverseHelper(probes, datPkg, entrezIds) : > No Entrez Gene ids left in universe > > Enter a frame number, or 0 to exit > > 1: hyperGTest(params) > 2: .valueClassTest(standardGeneric("hyperGTest"), "HyperGResultBase", "hyperGT > 3: is(object, Cl) > 4: is(object, Cl) > 5: universeBuilder(p) > 6: universeBuilder(p) > 7: getUniverseViaGo(p) > 8: getUniverseHelper(probes, datPkg, entrezIds) > > Selection: 8 > Called from: eval(expr, envir, enclos) > Browse[1]> ls() > [1] "datPkg" "entrezIds" "probes" "univ" > Browse[1]> datPkg > An object of class "ArabadopsisDatPkg" > Slot "name": > [1] "ragene10stv1" > > Browse[1]> entrezIds[1:5] > [1] "65049" "60444" "313914" "140941" "306868" > Browse[1]> probes[1:5] > [1] "10701636" "10701643" "10701654" "10701663" "10701679" > Browse[1]> univ > character(0) > Browse[1]> > > ------------------------------------------------------------ > Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry > Indiana University School of Medicine > > 15032 Hunter Court, Westfield, IN 46074 > > (317) 490-5129 Work, & Mobile & VoiceMail > (317) 399-1219 Home > Skype: mkimpel > > "The real problem is not whether machines think but whether men do." > -- B. F. Skinner > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > -- 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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