Hi all, I am having the same problem as Lavinia (below), namely, the arrayQualityMetrics() function failing on Windows. I'm using code directly from the vignette: > library("ALLMLL") > data("MLL.A") > library("arrayQualityMetrics") > arrayQualityMetrics(expressionset = MLL.A, + outdir = "MLL", + force = TRUE, + do.logtransform = TRUE) The result is: The report will be written into directory 'MLL'. KernSmooth 2.23 loaded Copyright M. P. Wand 1997-2009 (loaded the KernSmooth namespace) [[1]] [[2]] [[3]] Error in aqm.report.qm(p, obj[[i]], i, names(obj)[i]) : could not find function "svg" > traceback() 4: aqm.report.qm(p, obj[[i]], i, names(obj)[i]) 3: aqm.writereport(reporttitle, expressionset, obj) 2: arrayQualityMetrics(expressionset = MLL.A, outdir = "MLL", force = TRUE, do.logtransform = TRUE) 1: arrayQualityMetrics(expressionset = MLL.A, outdir = "MLL", force = TRUE, do.logtransform = TRUE) > sessionInfo() R version 2.12.0 (2010-10-15) Platform: i386-pc-mingw32/i386 (32-bit) locale: [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 [3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C [5] LC_TIME=English_United States.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] hgu133acdf_2.7.0 ALLMLL_1.2.8 arrayQualityMetrics_3.2.3 [4] vsn_3.18.0 affyPLM_1.26.0 preprocessCore_1.12.0 [7] gcrma_2.22.0 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_2.0.2 [5] Biostrings_2.18.2 DBI_0.2-5 genefilter_1.32.0 grid_2.12.0 [9] hwriter_1.3 IRanges_1.8.6 KernSmooth_2.23-4 lattice_0.19-13 [13] latticeExtra_0.6-14 limma_3.6.9 marray_1.28.0 RColorBrewer_1.0-2 [17] RSQLite_0.9-4 simpleaffy_2.26.1 splines_2.12.0 stats4_2.12.0 [21] survival_2.35-8 SVGAnnotation_0.7-2 tools_2.12.0 XML_3.2-0.2 [25] xtable_1.5-6 Thanks, Dan On Thu, Nov 18, 2010 at 11:14 PM, Lavinia Gordon wrote: > Hi Dan, > hmm, tried this, no luck: > > arrayQualityMetrics(expressionset = methylumi.eset,outdir = > "arrayQualityMetrics_patients", force = TRUE) > The report will be written into directory 'arrayQualityMetrics_patients'. > [[1]] > > [[2]] > > > Error in aqm.report.qm(p, obj[[i]], i, names(obj)[i]) : > could not find function "svg" > > > > sessionInfo() > R version 2.12.0 (2010-10-15) > Platform: i386-pc-mingw32/i386 (32-bit) > > locale: > [1] LC_COLLATE=English_Australia.1252 LC_CTYPE=English_Australia.1252 > LC_MONETARY=English_Australia.1252 > [4] LC_NUMERIC=C LC_TIME=English_Australia.1252 > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] arrayQualityMetrics_3.2.3 vsn_3.18.0 > affyPLM_1.26.0 preprocessCore_1.12.0 > [5] gcrma_2.22.0 affy_1.28.0 > SVGAnnotation_0.7-2 XML_3.2-0.1 > [9] Cairo_1.4-5 methylumi_1.4.0 > lumi_2.2.0 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_2.0.1 Biostrings_2.18.0 > [6] DBI_0.2-5 genefilter_1.32.0 grid_2.12.0 > hdrcde_2.15 hwriter_1.2 > [11] IRanges_1.8.2 KernSmooth_2.23-4 lattice_0.19-13 > latticeExtra_0.6-14 limma_3.6.4 > [16] marray_1.28.0 MASS_7.3-8 Matrix_0.999375-45 > mgcv_1.7-2 nlme_3.1-97 > [21] RColorBrewer_1.0-2 RSQLite_0.9-3 simpleaffy_2.26.0 > splines_2.12.0 stats4_2.12.0 > [26] survival_2.36-1 xtable_1.5-6 > > > > > Any ideas? > thanks > Lavinia. > > > On 19/11/2010 5:10 PM, Lavinia Gordon wrote: > > Thanks Dan, sorry I had missed the previous posts. > > On 19/11/2010 5:03 PM, Dan Tenenbaum wrote: > > > > On Thu, Nov 18, 2010 at 9:51 PM, Lavinia Gordon < > lavinia.gordon@mcri.edu.au> wrote: > >> Hi, >> I think there is a problem with the 2.7 version of arrayQualityMetrics. >> Following the example (in the script >> \R\R-2.12.0\library\arrayQualityMetrics\scripts\arrayQualityMetrics.R) >> >> > library("arrayQualityMetrics") >> Loading required package: affyPLM >> Loading required package: gcrma >> Loading required package: preprocessCore >> >> Attaching package: 'affyPLM' >> >> The following object(s) are masked from 'package:stats': >> >> resid, residuals, weights >> >> Loading required package: vsn >> > arrayQualityMetrics(expressionset = MLL.A, >> + outdir = "MLL", >> + force = TRUE, >> + do.logtransform = TRUE) >> The directory 'MLL' has been created. >> Error : cannot allocate vector of size 77.4 Mb >> KernSmooth 2.23 loaded >> Copyright M. P. Wand 1997-2009 >> (loaded the KernSmooth namespace) >> [[1]] >> >> [[2]] >> >> [[3]] >> >> Error in aqm.report.qm(p, obj[[i]], i, names(obj)[i]) : >> could not find function "svg" >> In addition: Warning message: >> In arrayQualityMetrics(expressionset = MLL.A, outdir = "MLL", force = >> TRUE, : >> Could not draw spatial distribution of intensities >> >> > traceback() >> 4: aqm.report.qm(p, obj[[i]], i, names(obj)[i]) >> 3: aqm.writereport(reporttitle, expressionset, obj) >> 2: arrayQualityMetrics(expressionset = MLL.A, outdir = "MLL", force = >> TRUE, >> do.logtransform = TRUE) >> 1: arrayQualityMetrics(expressionset = MLL.A, outdir = "MLL", force = >> TRUE, >> do.logtransform = TRUE) >> >> > sessionInfo() >> R version 2.12.0 (2010-10-15) >> Platform: i386-pc-mingw32/i386 (32-bit) >> >> locale: >> [1] LC_COLLATE=English_Australia.1252 LC_CTYPE=English_Australia.1252 >> LC_MONETARY=English_Australia.1252 >> [4] LC_NUMERIC=C LC_TIME=English_Australia.1252 >> >> attached base packages: >> [1] stats graphics grDevices utils datasets methods base >> >> other attached packages: >> [1] hgu133acdf_2.7.0 arrayQualityMetrics_3.2.0 vsn_3.18.0 >> affyPLM_1.26.0 >> [5] preprocessCore_1.12.0 gcrma_2.22.0 ALLMLL_1.2.8 >> affy_1.28.0 >> [9] 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_2.0.1 Biostrings_2.18.0 >> [6] DBI_0.2-5 genefilter_1.32.0 grid_2.12.0 >> hwriter_1.2 IRanges_1.8.2 >> [11] KernSmooth_2.23-4 lattice_0.19-13 latticeExtra_0.6-14 >> limma_3.6.4 marray_1.28.0 >> [16] RColorBrewer_1.0-2 RSQLite_0.9-3 simpleaffy_2.26.0 >> splines_2.12.0 stats4_2.12.0 >> [21] survival_2.36-1 SVGAnnotation_0.6-0 tools_2.12.0 >> XML_3.2-0.1 xtable_1.5-6 >> >> with regards >> >> Lavinia Gordon >> >> Hi Lavinia, > > This is a known issue that has come up with this package before on this > list. You need the current versions of arrayQualityMetrics (3.2.3) and > SVGAnnotation (0.7-2). > Try: > biocLite(c("arrayQualityMetrics","SVGAnnotation")) > > Dan > > > > -- > Senior Bioinformatics Officer > Murdoch Childrens Research Institute > Royal Children's Hospital > Flemington Road > Parkville > Victoria 3052 > Australiawww.mcri.edu.au > > > > -- > Senior Bioinformatics Officer > Murdoch Childrens Research Institute > Royal Children's Hospital > Flemington Road > Parkville > Victoria 3052 > Australiawww.mcri.edu.au > > [[alternative HTML version deleted]]