Dear all, I'm trying to run the arrayQualityMetrics function for the first time and an error comes out: > arrayQualityMetrics(RG, outdir="QCMetrics_onRG/", force=TRUE, do.logtransform=TRUE) The directory 'QCMetrics_onRG/' has been created. KernSmooth 2.23 loaded Copyright M. P. Wand 1997-2009 (loaded the KernSmooth namespace) [[1]] Error en aqm.report.qm(p, obj[[i]], i, names(obj)[i]) : no se pudo encontrar la función "svg" Además: Mensajes de aviso perdidos 1: The argument 'grouprep' of the function 'arrayQualityMetrics' is deprecated and will be ignored. Use 'intgroup' instead. 2: In dir.create(outdir, recursive = TRUE) : 'QCMetrics_onRG' already exists Here it is the traceback(): > traceback() 7: aqm.report.qm(p, obj[[i]], i, names(obj)[i]) 6: aqm.writereport(reporttitle, expressionset, obj) 5: arrayQualityMetrics(expressionset, outdir, force, do.logtransform, intgroup, spatial) 4: arrayQualityMetrics(expressionset, outdir, force, do.logtransform, intgroup, spatial) 3: .local(expressionset, outdir, force, do.logtransform, intgroup, spatial) 2: arrayQualityMetrics(RG, outdir = "QCMetrics_onRG_1/", force = TRUE, do.logtransform = TRUE) 1: arrayQualityMetrics(RG, outdir = "QCMetrics_onRG_1/", force = TRUE, do.logtransform = TRUE) and the sessionInfo(): > sessionInfo() R version 2.12.1 (2010-12-16) Platform: i386-pc-mingw32/i386 (32-bit) locale: [1] LC_COLLATE=Spanish_Spain.1252 LC_CTYPE=Spanish_Spain.1252 LC_MONETARY=Spanish_Spain.1252 LC_NUMERIC=C [5] LC_TIME=Spanish_Spain.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] arrayQualityMetrics_3.2.4 vsn_3.18.0 affyPLM_1.26.0 preprocessCore_1.12.0 gcrma_2.22.0 [6] affy_1.28.0 Biobase_2.10.0 loaded via a namespace (and not attached): [1] affyio_1.18.0 annotate_1.28.0 AnnotationDbi_1.12.0 beadarray_2.0.3 Biostrings_2.18.2 Cairo_1.4-6 DBI_0.2-5 [8] genefilter_1.32.0 grid_2.12.1 hwriter_1.3 IRanges_1.8.8 KernSmooth_2.23-4 lattice_0.19-17 latticeExtra_0.6-14 [15] limma_3.6.9 marray_1.28.0 RColorBrewer_1.0-2 RSQLite_0.9-4 simpleaffy_2.26.1 splines_2.12.1 stats4_2.12.1 [22] survival_2.36-2 SVGAnnotation_0.7-2 tools_2.12.1 XML_3.2-0.2 xtable_1.5-6 Anyone knows how could I fix it? Many thanks in advance! Best regards, Núria [[alternative HTML version deleted]]

Hi, On Mon, Feb 14, 2011 at 5:09 AM, <nqueralt at="" clinic.ub.es=""> wrote: > Dear all, > > I'm trying to run the arrayQualityMetrics function for the first time and an error comes out: > >> arrayQualityMetrics(RG, outdir="QCMetrics_onRG/", force=TRUE, do.logtransform=TRUE) > > The directory 'QCMetrics_onRG/' has been created. > > KernSmooth 2.23 loaded > > Copyright M. P. Wand 1997-2009 > > (loaded the KernSmooth namespace) > > [[1]] > > > > Error en aqm.report.qm(p, obj[[i]], i, names(obj)[i]) : > > ?no se pudo encontrar la funci?n "svg" My spanish is a bit rusty, but it looks like this is your problem. For some reason the "svg" function is not there, and I believe that it should be (I'm no R windows expert, though). Can you copy/paste the result you get when you call capabilities() from the R prompt. Eg. I get: R> capabilities() jpeg png tiff tcltk X11 aqua http/ftp sockets TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE libxml fifo cledit iconv NLS profmem cairo TRUE TRUE TRUE TRUE TRUE TRUE TRUE And I believe having the "cairo" value == TRUE is essential to have svg working. Maybe you need to install the "Cairo" library? http://cran.r-project.org/web/packages/Cairo/index.html Don't know ... not exactly sure. -- Steve Lianoglou Graduate Student: Computational Systems Biology ?| Memorial Sloan-Kettering Cancer Center ?| Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact

Dear N?ria thank you for the feedback! You have (at least) two options: 1. as Steve already said, get access to an R for which the 'svg' device is available (this is easy on Linux, but might be fiddly on Windows), or 2. install the Cairo package from CRAN, http://cran.r-project.org/web/packages/Cairo/index.html and then the development version of arrayQualityMetrics http://www.bioconductor.org/help/bioc- views/devel/bioc/html/arrayQualityMetrics.html One way to do this is to download the .zip files and then in R, choose the "Packages" menu and do "Install package from local zip file". The qualifications mentioned previously still apply: https://stat.ethz.ch/pipermail/bioconductor/2011-February/037779.html Thanks and best wishes Wolfgang nqueralt at clinic.ub.es scripsit 14/02/11 11:09: > Dear all, > > > > I'm trying to run the arrayQualityMetrics function for the first time and an error comes out: > > > >> arrayQualityMetrics(RG, outdir="QCMetrics_onRG/", force=TRUE, do.logtransform=TRUE) > > The directory 'QCMetrics_onRG/' has been created. > > KernSmooth 2.23 loaded > > Copyright M. P. Wand 1997-2009 > > (loaded the KernSmooth namespace) > > [[1]] > > > > Error en aqm.report.qm(p, obj[[i]], i, names(obj)[i]) : > > no se pudo encontrar la funci?n "svg" > > Adem?s: Mensajes de aviso perdidos > > 1: The argument 'grouprep' of the function 'arrayQualityMetrics' is deprecated and will be ignored. Use 'intgroup' instead. > > 2: In dir.create(outdir, recursive = TRUE) : > > 'QCMetrics_onRG' already exists > > > > Here it is the traceback(): > > > >> traceback() > > 7: aqm.report.qm(p, obj[[i]], i, names(obj)[i]) > > 6: aqm.writereport(reporttitle, expressionset, obj) > > 5: arrayQualityMetrics(expressionset, outdir, force, do.logtransform, > > intgroup, spatial) > > 4: arrayQualityMetrics(expressionset, outdir, force, do.logtransform, > > intgroup, spatial) > > 3: .local(expressionset, outdir, force, do.logtransform, intgroup, > > spatial) > > 2: arrayQualityMetrics(RG, outdir = "QCMetrics_onRG_1/", force = TRUE, > > do.logtransform = TRUE) > > 1: arrayQualityMetrics(RG, outdir = "QCMetrics_onRG_1/", force = TRUE, > > do.logtransform = TRUE) > > > > and the sessionInfo(): > > > >> sessionInfo() > > R version 2.12.1 (2010-12-16) > > Platform: i386-pc-mingw32/i386 (32-bit) > > > > locale: > > [1] LC_COLLATE=Spanish_Spain.1252 LC_CTYPE=Spanish_Spain.1252 LC_MONETARY=Spanish_Spain.1252 LC_NUMERIC=C > > [5] LC_TIME=Spanish_Spain.1252 > > > > attached base packages: > > [1] stats graphics grDevices utils datasets methods base > > > > other attached packages: > > [1] arrayQualityMetrics_3.2.4 vsn_3.18.0 affyPLM_1.26.0 preprocessCore_1.12.0 gcrma_2.22.0 > > [6] affy_1.28.0 Biobase_2.10.0 > > > > loaded via a namespace (and not attached): > > [1] affyio_1.18.0 annotate_1.28.0 AnnotationDbi_1.12.0 beadarray_2.0.3 Biostrings_2.18.2 Cairo_1.4-6 DBI_0.2-5 > > [8] genefilter_1.32.0 grid_2.12.1 hwriter_1.3 IRanges_1.8.8 KernSmooth_2.23-4 lattice_0.19-17 latticeExtra_0.6-14 > > [15] limma_3.6.9 marray_1.28.0 RColorBrewer_1.0-2 RSQLite_0.9-4 simpleaffy_2.26.1 splines_2.12.1 stats4_2.12.1 > > [22] survival_2.36-2 SVGAnnotation_0.7-2 tools_2.12.1 XML_3.2-0.2 xtable_1.5-6 > > > > Anyone knows how could I fix it? Many thanks in advance! > > > > Best regards, > > > > N?ria > > > > > [[alternative HTML version deleted]] > > > > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > 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