Dear All, I have been trying to use rMAT and its tutorial (http://wiki.rglab.org/index.php?title=Public:RMAT ). I am working with MacOSX and a recent R version. I was able to install rMAT (at least it loads correctly in R when launching it from the package manager window) as well as the data set which is used in the tutorial. I can load the different datasets separately, but when I try to combine them into a single variable, I get this error message (see below). I do not know what is going on.. R seems to be unable to convert some variables (see error highlighted in red). I would appreciate any help. Thanks in advance, Patrick R version 2.9.1 (2009-06-26) Copyright (C) 2009 The R Foundation for Statistical Computing ISBN 3-900051-07-0 R est un logiciel libre livré sans AUCUNE GARANTIE. Vous pouvez le redistribuer sous certaines conditions. Tapez 'license()' ou 'licence()' pour plus de détails. R est un projet collaboratif avec de nombreux contributeurs. Tapez 'contributors()' pour plus d'information et 'citation()' pour la façon de le citer dans les publications. Tapez 'demo()' pour des démonstrations, 'help()' pour l'aide en ligne ou 'help.start()' pour obtenir l'aide au format HTML. Tapez 'q()' pour quitter R. [R.app GUI 1.28 (5444) i386-apple-darwin8.11.1] Attachement du package : 'gsl' The following object(s) are masked from package:stats : sd Le chargement a nécessité le package : biomaRt Le chargement a nécessité le package : grid celA<-c("MCF_ER_A1.CEL","MCF_ER_A3.CEL", "MCF_ER_A4.CEL", "MCF_INP_A1.CEL", "MCF_INP_A3.CEL","MCF_INP_A4.CEL") > ERA<-BPMAPCelParser(bpmapA, celA, seqName="chr2") > bpmapB<-"P1_CHIP_B.Anti-Sense.hs.NCBIv35.NR.bpmap" > celB<-c("MCF_ER_B1.CEL","MCF_ER_B3.CEL", "MCF_ER_B4.CEL", "MCF_INP_B1.CEL", "MCF_INP_B3.CEL","MCF_INP_B4.CEL") > ERB<-BPMAPCelParser(bpmapB, celB, seqName="chr2") > bpmapC<-"P1_CHIP_C.Anti-Sense.hs.NCBIv35.NR.bpmap" > celC<-c("MCF_ER_C1.CEL","MCF_ER_C3.CEL", "MCF_ER_C4.CEL", "MCF_INP_C1.CEL", "MCF_INP_C3.CEL","MCF_INP_C4.CEL") > ERC<-BPMAPCelParser(bpmapC, celC, seqName="chr2") Erreur dans .Method(..., deparse.level = deparse.level) : pas de méthode pour convertir automatiquement cette classe S4 en vecteur > sessionInfo() R version 2.9.1 (2009-06-26) i386-apple-darwin8.11.1 locale: fr_CH.UTF-8/fr_CH.UTF-8/C/C/fr_CH.UTF-8/fr_CH.UTF-8 attached base packages: [1] grid stats graphics grDevices utils datasets methods base other attached packages: [1] GenomeGraphs_1.4.1 biomaRt_2.0.0 gsl_1.8-14 rMAT_1.1.2 loaded via a namespace (and not attached): [1] affxparser_1.16.0 Biobase_2.4.1 RCurl_0.98-1 XML_2.6-0 [[alternative HTML version deleted]]

Dear Patrick the first thing you could do is upgrade your R and rMAT. I doubt anyone here is interested in debugging older versions. The last release version of rMAT was 2.3.4, you're using 1.1.2. And btw a new release is imminent: http://wiki.fhcrc.org/bioc/BioC_2.6_Release_Schedule Best wishes Wolfgang Schorderet ha scritto: > Dear All, > > I have been trying to use rMAT and its tutorial (http://wiki.rglab.org/index.php?title=Public:RMAT > ). I am working with MacOSX and a recent R version. I was able to > install rMAT (at least it loads correctly in R when launching it from > the package manager window) as well as the data set which is used in > the tutorial. I can load the different datasets separately, but when I > try to combine them into a single variable, I get this error message > (see below). I do not know what is going on.. R seems to be unable to > convert some variables (see error highlighted in red). > > I would appreciate any help. Thanks in advance, > > Patrick > > > > R version 2.9.1 (2009-06-26) > Copyright (C) 2009 The R Foundation for Statistical Computing > ISBN 3-900051-07-0 > > R est un logiciel libre livr? sans AUCUNE GARANTIE. > Vous pouvez le redistribuer sous certaines conditions. > Tapez 'license()' ou 'licence()' pour plus de d?tails. > > R est un projet collaboratif avec de nombreux contributeurs. > Tapez 'contributors()' pour plus d'information et > 'citation()' pour la fa?on de le citer dans les publications. > > Tapez 'demo()' pour des d?monstrations, 'help()' pour l'aide > en ligne ou 'help.start()' pour obtenir l'aide au format HTML. > Tapez 'q()' pour quitter R. > > [R.app GUI 1.28 (5444) i386-apple-darwin8.11.1] > > > > > Attachement du package : 'gsl' > > > The following object(s) are masked from package:stats : > > sd > > Le chargement a n?cessit? le package : biomaRt > Le chargement a n?cessit? le package : grid > > > celA<-c("MCF_ER_A1.CEL","MCF_ER_A3.CEL", "MCF_ER_A4.CEL", > "MCF_INP_A1.CEL", "MCF_INP_A3.CEL","MCF_INP_A4.CEL") > > ERA<-BPMAPCelParser(bpmapA, celA, seqName="chr2") > > bpmapB<-"P1_CHIP_B.Anti-Sense.hs.NCBIv35.NR.bpmap" > > celB<-c("MCF_ER_B1.CEL","MCF_ER_B3.CEL", "MCF_ER_B4.CEL", > "MCF_INP_B1.CEL", "MCF_INP_B3.CEL","MCF_INP_B4.CEL") > > ERB<-BPMAPCelParser(bpmapB, celB, seqName="chr2") > > bpmapC<-"P1_CHIP_C.Anti-Sense.hs.NCBIv35.NR.bpmap" > > celC<-c("MCF_ER_C1.CEL","MCF_ER_C3.CEL", "MCF_ER_C4.CEL", > "MCF_INP_C1.CEL", "MCF_INP_C3.CEL","MCF_INP_C4.CEL") > > ERC<-BPMAPCelParser(bpmapC, celC, seqName="chr2") > > > Erreur dans .Method(..., deparse.level = deparse.level) : > pas de m?thode pour convertir automatiquement cette classe S4 en > vecteur > > > > sessionInfo() > R version 2.9.1 (2009-06-26) > i386-apple-darwin8.11.1 > > locale: > fr_CH.UTF-8/fr_CH.UTF-8/C/C/fr_CH.UTF-8/fr_CH.UTF-8 > > attached base packages: > [1] grid stats graphics grDevices utils datasets > methods base > > other attached packages: > [1] GenomeGraphs_1.4.1 biomaRt_2.0.0 gsl_1.8-14 rMAT_1.1.2 > > loaded via a namespace (and not attached): > [1] affxparser_1.16.0 Biobase_2.4.1 RCurl_0.98-1 XML_2.6-0 > > > > [[alternative HTML version deleted]] > > > > -------------------------------------------------------------------- ---- > > _______________________________________________ > 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 Huber EMBL http://www.embl.de/research/units/genome_biology/huber