OK this was a glaring mistake from mine. I sincerely apologyze for disturbing with such a stupid thing. I promise I'll pay more attention now and think better before asking anything. Sorry, Cl?mentine On Fri, 12 Nov 2010 13:16:01 -0500, Sean Davis <sdavis2 at="" mail.nih.gov=""> wrote: > 2010/11/12 Cl?mentine Dressaire <clementinedressaire at="" itqb.unl.pt=""> > >> >> Hello again, >> >> >> >> I have completely forgotten to copy my session informations... >> >> >> >> > sessionInfo() >> >> R version 2.12.0 (2010-10-15) >> >> Platform: i386-pc-mingw32/i386 (32-bit) >> >> >> >> locale: >> >> [1] LC_COLLATE=French_France.1252 LC_CTYPE=French_France.1252 >> >> LC_MONETARY=French_France.1252 >> >> [4] LC_NUMERIC=C LC_TIME=French_France.1252 >> >> >> >> attached base packages: >> >> [1] stats graphics grDevices utils datasets methods base >> >> >> >> other attached packages: >> >> [1] ecoli2cdf_2.6.0 gage_2.0.0 multtest_2.6.0 >> >> ecoli2.db_2.4.7 org.EcK12.eg.db_2.4.6 >> >> [6] simpleaffy_2.26.0 gcrma_2.22.0 genefilter_1.32.0 >> >> annotate_1.28.0 biomaRt_2.6.0 >> >> [11] annaffy_1.22.0 KEGG.db_2.4.5 GO.db_2.4.5 >> >> lattice_0.19-13 affy_1.28.0 >> >> [16] limma_3.6.0 GOstats_2.16.0 RSQLite_0.9-2 >> >> DBI_0.2-5 graph_1.28.0 >> >> [21] Category_2.16.0 AnnotationDbi_1.12.0 Biobase_2.10.0 >> >> >> >> loaded via a namespace (and not attached): >> >> [1] affyio_1.18.0 Biostrings_2.18.0 grid_2.12.0 >> >> GSEABase_1.12.0 IRanges_1.8.0 >> >> [6] MASS_7.3-8 preprocessCore_1.12.0 RBGL_1.25.1 >> >> RCurl_1.4-4.1 splines_2.12.0 >> >> [11] survival_2.35-8 tools_2.12.0 XML_3.2-0.1 >> >> xtable_1.5-6 >> >> >> >> >> >> As for an example if I use the following vector of EntrezGeneIds I get a >> >> similar error message: >> >> >> >> >> >ex=c(947043,948258,2847747,2847746,946713,948679,948192,944872,946844 ,946841) >> >> > ex >> >> [1] 947043 948258 2847747 2847746 946713 948679 948192 944872 >> >> 946844 946841 >> >> > makeGOGraph(ex,ontology="BP",removeRoot=T,mapfun=NULL,chip=ecoli2.db) >> >> >> >> Erreur dans makeGOGraph(ex, ontology = "BP", removeRoot = T, mapfun = >> >> NULL, : >> >> argument(s) inutilis?(s) (ontology = "BP") >> >> > Try using "Ontology" instead of "ontology" for the argument. Note that the > capital letter is needed. > > Sean > > > >> >> >> >> >> Cl?mentine >> >> >> >> >> >> >> >> On Fri, 12 Nov 2010 09:12:18 -0800, Marc Carlson <mcarlson at="" fhcrc.org=""> >> >> wrote: >> >> > Hi Cl?mentine, >> >> > >> >> > Could you please give us your sessionInfo() and a reproducible example? >> >> > That would allow us to be able to really find out what is happening >> >> > here. You might want find it helpful to have a peek at the posting >> >> > guide here: >> >> > >> >> > http://www.bioconductor.org/help/mailing-list/posting-guide/ >> >> > >> >> > >> >> > Marc >> >> > >> >> > >> >> > >> >> > >> >> > On 11/12/2010 07:51 AM, Cl?mentine Dressaire wrote: >> >> >> Dear BioC users, >> >> >> >> >> >> >> >> >> >> >> >> I am trying to construct a GOgraph using a gene list (overgenes[,3]) >> >> of >> >> >> >> >> >> messengers that I previously identified as overexpressed in the >> >> >> condition I >> >> >> >> >> >> was interested in. I previoulsy used this same gene list to perform >> >> >> >> >> >> hypergeometric tests and it worked well. >> >> >> >> >> >> >> >> >> >> >> >> With makeGOgraph I systematically get the following error message, >> >> >> >> >> >> whichever ontology type I try to use: >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> makeGOGraph(overgenes[,3],ontology="BP",removeRoot=F,mapfun=NULL,chip= ecoli2.db) >> >> >> >> >> >> >> >> >> >> >> >> Erreur dans makeGOGraph(overgenes[, 3], ontology = "BP", >> >> removeRoot >> >> >> = >> >> >> >> >> >> F, : >> >> >> >> >> >> argument(s) inutilis?(s) (ontology = "BP") >> >> >> >> >> >> >> >> >> >> >> >> I wonder wether this could be due to the fact that some of the genes >> >> in >> >> >> >> >> >> the list do not have GO annotation...(then does it mean that I have to >> >> >> >> >> >> eliminate them? If so what would be the simplest way?) >> >> >> >> >> >> >> >> >> >> >> >> Does anyone can throw light on this issue for me? >> >> >> >> >> >> >> >> >> >> >> >> Many thanks for your help, >> >> >> >> >> >> >> >> >> >> >> >> Cl?mentine >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> > >> >> > _______________________________________________ >> >> > 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 >> >> >> >> -- >> >> Cl?mentine Dressaire >> >> Post-doctoral research fellow >> >> Control of gene expression lab >> >> ITQB - Instituto de Tecnologia Qu?mica e Biol?gica >> >> Apartado 127, Av. da Rep?blica >> >> 2780-157 Oeiras >> >> Portugal >> >> +351 214469562 >> >> _______________________________________________ >> 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 -- Cl?mentine Dressaire Post-doctoral research fellow Control of gene expression lab ITQB - Instituto de Tecnologia Qu?mica e Biol?gica Apartado 127, Av. da Rep?blica 2780-157 Oeiras Portugal +351 214469562