error with ontoCompare (goTools)
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@wolfgang-raffelsberger-1805
Last seen 6.8 years ago
Dear list, I'm interested in making a graph (pie-chart or similar) showing the different GO ontologies one may get from a list of genes (in my case a list of Affymetrix probe-sets). In this context it might be good only to compare a given level of GO-ontologies (to avoid redundancies with terms closer to the root), ideally I'd like use something close to GO- slim. It looks like that goTools allows to do something close to what I'm interested (without the GOslim...). So I tried to use goTools but running the code from the documentation (as suggested in ?ontoCompare ) I got the following error : library(goTools) library(GO.db) data(probeID) affylist2 <- list(L4 <- affylist[[1]][1:5], L5 <- affylist[[2]][1:4]) # shorter list just for testing ... res0 <- ontoCompare(affylist2, probeType = "hgu133a", plot=T) and I get the following (error) message : Starting ontoCompare... Error in FUN(X[[1L]], ...) : unused argument(s) (list(`GO:0000001` = <s4 object="" of="" class="" "goterms"="">, `GO:0000002` = <s4 object="" of="" class="" "goterms"="">, `GO:0000003` = <s4 object="" of="" class="" "goterms"="">, `GO:0000006` = <s4 object="" of="" class="" "goterms"="">, `GO:0000007` = <s4 object="" of="" class="" "goterms"="">, `GO:0000009` = <s4 object="" of="" class="" ...="" am="" i="" missing="" somthing="" ?="" other="" suggestions="" ?="" thank's="" for="" any="" hints,="" wolfgang="" just="" for="" completeness:="" sessioninfo()="" r="" version="" 2.8.1="" (2008-12-22)="" i386-pc-mingw32="" locale:="" lc_collate="French_France.1252;LC_CTYPE=French_France.1252;LC_MONETARY=" french_france.1252;lc_numeric="C;LC_TIME=French_France.1252" attached="" base="" packages:="" [1]="" tools="" stats="" graphics="" grdevices="" datasets="" tcltk="" utils="" methods="" base="" other="" attached="" packages:="" [1]="" hgu133a.db_2.2.5="" annotate_1.20.1="" xtable_1.5-4="" gotools_1.16.0="" go.db_2.2.5="" [6]="" rsqlite_0.7-1="" dbi_0.2-4="" annotationdbi_1.4.2="" biobase_2.2.1="" svsocket_0.9-5="" [11]="" svio_0.9-5="" r2html_1.59="" svmisc_0.9-5="" svide_0.9-5="" .="" .="" .="" .="" .="" .="" .="" .="" .="" .="" .="" .="" .="" .="" .="" .="" .="" .="" .="" .="" .="" .="" .="" .="" .="" .="" .="" .="" .="" .="" .="" .="" .="" .="" .="" .="" wolfgang="" raffelsberger,="" phd="" laboratoire="" de="" bioinformatique="" et="" g?nomique="" int?gratives="" cnrs="" umr7104,="" igbmc="" 1="" rue="" laurent="" fries,="" 67404="" illkirch="" strasbourg,="" france="" tel="" (+33)="" 388="" 65="" 3300="" fax="" (+33)="" 388="" 65="" 3276="" wolfgang.raffelsberger="" (at)="" igbmc.fr="" <="" div="">
GO hgu133a graph goTools GO hgu133a graph goTools • 730 views
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@martin-morgan-1513
Last seen 8 hours ago
United States
Hi Wolfgang -- Wolfgang Raffelsberger <wraff at="" titus.u-strasbg.fr=""> writes: > Just as additional information : > I found out that this problem might to be specific to Windows (with > R-2.8.0). I managed to run the same code on Linux with R-2.8.0 without > the error message ... I think this is an issue with the interaction between annotate and goTools. Both define a function getOntology. I guess your search() path has annotate in front of goTools. goTools does not have a name space. When it looks for getOntology, it finds the version that is 'first' on the search path. This is the annotate version. Two short term solutions are to arrange your search path so that goTools is before annotate (e.g., by library(annotate) before library(goTools)) or temporarily masking the annotate version of the function > getOntology <- goTools::getOntology > res0 <- ontoCompare(affylist2, probeType = "hgu133a", plot=T) > rm(getOntology) A longer term solution is for the maintainer of goTools (cc'd) to add a name space (perhaps using the experimental package codetoolsBioC available in the bioc devel repository to help identify appropriate imports) so that code in the goTools package is guaranteed to find the right version of the function. Martin > Wolfgang > > > sessionInfo() > R version 2.8.0 (2008-10-20) > x86_64-unknown-linux-gnu > > locale: > C > > attached base packages: > [1] tools stats graphics grDevices utils datasets > methods [8] base > > other attached packages: > [1] hgu133a.db_2.2.5 goTools_1.16.0 GO.db_2.2.5 [4] > RSQLite_0.7-1 DBI_0.2-4 AnnotationDbi_1.4.1 > [7] Biobase_2.2.1 > > > > Wolfgang Raffelsberger a ?crit : >> Dear list, >> I'm interested in making a graph (pie-chart or similar) showing the >> different GO ontologies one may get from a list of genes (in my case >> a list of Affymetrix probe-sets). In this context it might be good >> only to compare a given level of GO-ontologies (to avoid >> redundancies with terms closer to the root), ideally I'd like use >> something close to GO-slim. >> >> It looks like that goTools allows to do something close to what I'm >> interested (without the GOslim...). >> So I tried to use goTools but running the code from the >> documentation (as suggested in ?ontoCompare ) I got the following >> error : >> >> library(goTools) >> library(GO.db) >> data(probeID) >> affylist2 <- list(L4 <- affylist[[1]][1:5], L5 <- >> affylist[[2]][1:4]) # shorter list just for testing ... >> res0 <- ontoCompare(affylist2, probeType = "hgu133a", plot=T) >> >> and I get the following (error) message : >> >> Starting ontoCompare... >> Error in FUN(X[[1L]], ...) : >> unused argument(s) (list(`GO:0000001` = <s4 object="" of="" class="">> "GOTerms">, `GO:0000002` = <s4 object="" of="" class="" "goterms"="">, >> GO:0000003` = <s4 object="" of="" class="" "goterms"="">, `GO:0000006` = <s4>> object of class "GOTerms">, `GO:0000007` = <s4 object="" of="" class="">> "GOTerms">, `GO:0000009` = <s4 object="" of="" class="" ...="">> >> Am I missing somthing ? >> Other suggestions ? >> >> Thank's for any hints, >> Wolfgang >> >> >> Just for completeness: >> sessionInfo() >> >> R version 2.8.1 (2008-12-22) >> i386-pc-mingw32 >> >> locale: >> LC_COLLATE=French_France.1252;LC_CTYPE=French_France.1252;LC_MONETA RY=French_France.1252;LC_NUMERIC=C;LC_TIME=French_France.1252 >> >> >> attached base packages: >> [1] tools stats graphics grDevices datasets tcltk >> utils methods base other attached packages: >> [1] hgu133a.db_2.2.5 annotate_1.20.1 xtable_1.5-4 >> goTools_1.16.0 GO.db_2.2.5 [6] RSQLite_0.7-1 >> DBI_0.2-4 AnnotationDbi_1.4.2 Biobase_2.2.1 >> svSocket_0.9-5 [11] svIO_0.9-5 R2HTML_1.59 >> svMisc_0.9-5 svIDE_0.9-5 >> >> > > . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . > Wolfgang Raffelsberger, PhD > Laboratoire de BioInformatique et G?nomique Int?gratives > CNRS UMR7104, IGBMC 1 rue Laurent Fries, 67404 Illkirch Strasbourg, > France > Tel (+33) 388 65 3300 Fax (+33) 388 65 3276 > wolfgang.raffelsberger (at) igbmc.fr > > _______________________________________________ > 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 -- Martin Morgan Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M2 B169 Phone: (206) 667-2793
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@wolfgang-raffelsberger-1805
Last seen 6.8 years ago
Just as additional information : I found out that this problem might to be specific to Windows (with R-2.8.0). I managed to run the same code on Linux with R-2.8.0 without the error message ... Wolfgang > sessionInfo() R version 2.8.0 (2008-10-20) x86_64-unknown-linux-gnu locale: C attached base packages: [1] tools stats graphics grDevices utils datasets methods [8] base other attached packages: [1] hgu133a.db_2.2.5 goTools_1.16.0 GO.db_2.2.5 [4] RSQLite_0.7-1 DBI_0.2-4 AnnotationDbi_1.4.1 [7] Biobase_2.2.1 Wolfgang Raffelsberger a ?crit : > Dear list, > I'm interested in making a graph (pie-chart or similar) showing the > different GO ontologies one may get from a list of genes (in my case a > list of Affymetrix probe-sets). In this context it might be good only > to compare a given level of GO-ontologies (to avoid redundancies with > terms closer to the root), ideally I'd like use something close to > GO-slim. > > It looks like that goTools allows to do something close to what I'm > interested (without the GOslim...). > So I tried to use goTools but running the code from the documentation > (as suggested in ?ontoCompare ) I got the following error : > > library(goTools) > library(GO.db) > data(probeID) > affylist2 <- list(L4 <- affylist[[1]][1:5], L5 <- > affylist[[2]][1:4]) # shorter list just for testing ... > res0 <- ontoCompare(affylist2, probeType = "hgu133a", plot=T) > > and I get the following (error) message : > > Starting ontoCompare... > Error in FUN(X[[1L]], ...) : > unused argument(s) (list(`GO:0000001` = <s4 object="" of="" class=""> "GOTerms">, `GO:0000002` = <s4 object="" of="" class="" "goterms"="">, > `GO:0000003` = <s4 object="" of="" class="" "goterms"="">, `GO:0000006` = <s4> object of class "GOTerms">, `GO:0000007` = <s4 object="" of="" class=""> "GOTerms">, `GO:0000009` = <s4 object="" of="" class="" ...=""> > Am I missing somthing ? > Other suggestions ? > > Thank's for any hints, > Wolfgang > > > Just for completeness: > sessionInfo() > > R version 2.8.1 (2008-12-22) > i386-pc-mingw32 > > locale: > LC_COLLATE=French_France.1252;LC_CTYPE=French_France.1252;LC_MONETAR Y=French_France.1252;LC_NUMERIC=C;LC_TIME=French_France.1252 > > > attached base packages: > [1] tools stats graphics grDevices datasets tcltk > utils methods base > other attached packages: > [1] hgu133a.db_2.2.5 annotate_1.20.1 xtable_1.5-4 > goTools_1.16.0 GO.db_2.2.5 [6] RSQLite_0.7-1 > DBI_0.2-4 AnnotationDbi_1.4.2 Biobase_2.2.1 > svSocket_0.9-5 [11] svIO_0.9-5 R2HTML_1.59 > svMisc_0.9-5 svIDE_0.9-5 > > . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Wolfgang Raffelsberger, PhD Laboratoire de BioInformatique et G?nomique Int?gratives CNRS UMR7104, IGBMC 1 rue Laurent Fries, 67404 Illkirch Strasbourg, France Tel (+33) 388 65 3300 Fax (+33) 388 65 3276 wolfgang.raffelsberger (at) igbmc.fr
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Alex Sanchez ▴ 90
@alex-sanchez-3227
Last seen 6.8 years ago
Hi WolfgangYou may want to try the 'goProfiles' package which is intended to do exactly what you're asking for, that is comparing two gene lists at a given level of the GO.I'd be happy to help if there appear any problems or to (try to) adapt any improvements you may suggest.BestAlex--------------------------------------------------- Alex S?nchezStatistics Department. University of Barcelona. Facultat de Biologia UB. Avda Diagonal 645. 08028 Barcelona. Spainmail asanchez_at_ub.eduStatistics and Bioinformatics UnitInstitut de Recerca. Hospital Universitari Vall 'HebronPasseig Vall d'Hebron 112-119. 08034 Barcelonamail asanchez_at_ir.vhebron.net-------------------------------------------- -------->Dear list, >I'm interested in making a graph (pie-chart or similar) showing the >different GO ontologies one may get from a list of genes (in my case a >list of Affymetrix probe-sets). In this context it might be good only >to compare a given level of GO-ontologies (to avoid redundancies with >terms closer to the root), ideally I'd like use something close to GO-slim. >It looks like that goTools allows to do something close to what I'm >interested (without the GOslim...). >So I tried to use goTools but running the code from the documentation >(as suggested in ?ontoCompare ) I got the following error : >library(goTools) >library(GO.db) >data(probeID) > affylist2 <- list(L4 <- affylist[[1]][1:5], L5 <- affylist[[2]][1:4]) ># shorter list just for testing ... > res0 <- ontoCompare(affylist2, probeType = "hgu133a", plot=T) >and I get the following (error) message : >Starting ontoCompare... >Error in FUN(X[[1L]], ...) : > unused argument(s) (list(`GO:0000001` = <s4 object="" of="" class="">"GOTerms">, `GO:0000002` = <s4 object="" of="" class="" "goterms"="">, `GO:0000003` >= <s4 object="" of="" class="" "goterms"="">, `GO:0000006` = <s4 object="" of="" class="">"GOTerms">, `GO:0000007` = <s4 object="" of="" class="" "goterms"="">, `GO:0000009` >= <s4 object="" of="" class="" ...="">Am I missing somthing ? >Other suggestions ? >Thank's for any hints, >Wolfgang > > >Just for completeness: >sessionInfo() > >R version 2.8.1 (2008-12-22) >i386-pc-mingw32 > >locale: >LC_COLLATE=French_France.1252;LC_CTYPE=French_France.1252;LC_MONETARY =French_France.1252;LC_NUMERIC=C;LC_TIME=French_France.1252 > >attached base packages: >[1] tools stats graphics grDevices datasets tcltk >utils methods base > >other attached packages: > [1] hgu133a.db_2.2.5 annotate_1.20.1 xtable_1.5-4 >goTools_1.16.0 GO.db_2.2.5 > [6] RSQLite_0.7-1 DBI_0.2-4 AnnotationDbi_1.4.2 >Biobase_2.2.1 svSocket_0.9-5 >[11] svIO_0.9-5 R2HTML_1.59 svMisc_0.9-5 >svIDE_0.9-5 > > > >. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . >Wolfgang Raffelsberger, PhD >Laboratoire de BioInformatique et G?nomique Int?gratives >CNRS UMR7104, IGBMC >1 rue Laurent Fries, 67404 Illkirch Strasbourg, France >Tel (+33) 388 65 3300 Fax (+33) 388 65 3276 >wolfgang.raffelsberger (at) igbmc.fr > >
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Alex Sanchez ▴ 90
@alex-sanchez-3227
Last seen 6.8 years ago
Hello Wolfgang I think you have found a bug which I skipped when moving from the old annotation system to the current .db based one. The problem seems to be simply that the internal affy-entrez conversion function is not working properly so you must convert it yourself before you call "basicProfile" The following should work while I solve the problem and update the package require(goProfiles) require(mouse4302.db) require(org.Mm.eg.db) affyPs <- c("1415670_at","1415671_at","1415672_at","1415673_at","1415675_at","14 15676_a_at","1415677_at","1415678_at","1415679_at") require(annotate) entrezs <- getEG (affyPs, "mouse4302.db") affy.MF <- basicProfile(entrezs, orgPackage = "org.Mm.eg.db", anotPackage="mouse4302.db", onto = "MF", level = 2) # "Entrez identifiers are the default printProfiles(affy.MF) Alex ...................................................................... ........................................ Alex S?nchez. Statistics Department. University of Barcelona. Facultat de Biologia UB. Avda Diagonal 645. 08028 Barcelona. Spain asanchez_at_ub.edu Statistics and Bioinformatics Unit Institut de Recerca. Hospital Universitari Vall 'Hebron Passeig Vall d'Hebron 112-119. 08034 Barcelona asanchez_at_ir.vhebron.net ...................................................................... ......................................... ----- Original Message ----- From: "Wolfgang Raffelsberger" <wraff@titus.u-strasbg.fr> To: "Alex Sanchez" <asanchez at="" ub.edu=""> Sent: Monday, January 19, 2009 6:40 PM Subject: Re: [BioC] error with ontoCompare (goTools) > Dear Alex, > > thank you for you interesting mail. > I tried with mouse affy probe-sets but I'm stuck with an error- message, > see the following code : > > require(goProfiles) > require(mouse4302.db) > require(org.Mm.eg.db) > # below : some IDs from from Affymetrix mouse4302 array > affyPs <- > c("1415670_at","1415671_at","1415672_at","1415673_at","1415675_at"," 1415676_a_at","1415677_at","1415678_at","1415679_at") > affy.MF <- basicProfile(affyPs, idType="BioCprobes", orgPackage = > "org.Mm.eg.db", anotPackage="mouse4302.db", onto = "MF", level = 2) > # here I get : > Error in eval(expr, envir, enclos) : > object "mouse4302.dbENTREZID" not found > # however, I don't see a package like this on the bioconductor web- site > > Have you any ideas/suggestions what I might be doing wrong ? > Thank's in advance, > Wolfgang > > > # for completeness ... > sessionInfo() > > R version 2.8.1 (2008-12-22) > i386-pc-mingw32 > > locale: > LC_COLLATE=French_France.1252;LC_CTYPE=French_France.1252;LC_MONETAR Y=French_France.1252;LC_NUMERIC=C;LC_TIME=French_France.1252 > > attached base packages: > [1] tools stats graphics grDevices datasets tcltk utils > methods base > other attached packages: > [1] org.Mm.eg.db_2.2.6 org.Hs.eg.db_2.2.6 mouse4302.db_2.2.5 > goProfiles_1.4.0 GO.db_2.2.5 RSQLite_0.7-1 [7] DBI_0.2-4 > AnnotationDbi_1.4.2 Biobase_2.2.1 svSocket_0.9-5 svIO_0.9-5 > R2HTML_1.59 [13] svMisc_0.9-5 svIDE_0.9-5 > > Alex Sanchez a ?crit : >> Hi WolfgangYou may want to try the 'goProfiles' package which is intended >> to do exactly what you're asking for, that is comparing two gene lists at >> a given level of the GO.I'd be happy to help if there appear any problems >> or to (try to) adapt any improvements you may >> suggest.BestAlex--------------------------------------------------- Alex >> S?nchezStatistics Department. University of Barcelona. Facultat de >> Biologia UB. Avda Diagonal 645. 08028 Barcelona. Spainmail >> asanchez_at_ub.eduStatistics and Bioinformatics UnitInstitut de Recerca. >> Hospital Universitari Vall 'HebronPasseig Vall d'Hebron 112-119. 08034 >> Barcelonamail >> asanchez_at_ir.vhebron.net----------------------------------------- ----------->Dear >> list, >>> I'm interested in making a graph (pie-chart or similar) showing the >>> different GO ontologies one may get from a list of genes (in my case a >>> list of Affymetrix probe-sets). In this context it might be good only >>> to compare a given level of GO-ontologies (to avoid redundancies with >>> terms closer to the root), ideally I'd like use something close to >>> GO-slim. >> >>> It looks like that goTools allows to do something close to what I'm >>> interested (without the GOslim...). >>> So I tried to use goTools but running the code from the documentation >>> (as suggested in ?ontoCompare ) I got the following error : >> >>> library(goTools) >>> library(GO.db) >>> data(probeID) >>> affylist2 <- list(L4 <- affylist[[1]][1:5], L5 <- affylist[[2]][1:4]) >>> # shorter list just for testing ... >>> res0 <- ontoCompare(affylist2, probeType = "hgu133a", plot=T) >> >>> and I get the following (error) message : >> >>> Starting ontoCompare... >>> Error in FUN(X[[1L]], ...) : >>> unused argument(s) (list(`GO:0000001` = <s4 object="" of="" class="">>> "GOTerms">, `GO:0000002` = <s4 object="" of="" class="" "goterms"="">, `GO:0000003` >>> = <s4 object="" of="" class="" "goterms"="">, `GO:0000006` = <s4 object="" of="" class="">>> "GOTerms">, `GO:0000007` = <s4 object="" of="" class="" "goterms"="">, `GO:0000009` >>> = <s4 object="" of="" class="" ...="">> >>> Am I missing somthing ? >>> Other suggestions ? >> >>> Thank's for any hints, >>> Wolfgang >>> >>> >>> Just for completeness: >>> sessionInfo() >>> >>> R version 2.8.1 (2008-12-22) >>> i386-pc-mingw32 >>> >>> locale: >>> LC_COLLATE=French_France.1252;LC_CTYPE=French_France.1252;LC_MONET ARY=French_France.1252;LC_NUMERIC=C;LC_TIME=French_France.1252 >>> >>> attached base packages: >>> [1] tools stats graphics grDevices datasets tcltk >>> utils methods base >>> >>> other attached packages: >>> [1] hgu133a.db_2.2.5 annotate_1.20.1 xtable_1.5-4 >>> goTools_1.16.0 GO.db_2.2.5 >>> [6] RSQLite_0.7-1 DBI_0.2-4 AnnotationDbi_1.4.2 >>> Biobase_2.2.1 svSocket_0.9-5 >>> [11] svIO_0.9-5 R2HTML_1.59 svMisc_0.9-5 >>> svIDE_0.9-5 >>> >>> >>> >>> . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . >>> Wolfgang Raffelsberger, PhD >>> Laboratoire de BioInformatique et G?nomique Int?gratives >>> CNRS UMR7104, IGBMC >>> 1 rue Laurent Fries, 67404 Illkirch Strasbourg, France >>> Tel (+33) 388 65 3300 Fax (+33) 388 65 3276 >>> wolfgang.raffelsberger (at) igbmc.fr >>> >>> >> >> _______________________________________________ >> 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 >> >> > > > -- > . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . > Wolfgang Raffelsberger, PhD > Laboratoire de BioInformatique et G?nomique Int?gratives > CNRS UMR7104, IGBMC 1 rue Laurent Fries, 67404 Illkirch Strasbourg, > France > Tel (+33) 388 65 3300 Fax (+33) 388 65 3276 > http://www-bio3d-igbmc.u-strasbg.fr/~wraff > wolfgang.raffelsberger at igbmc.fr > > >
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