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 <mailto: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 Australia www.mcri.edu.au [[alternative HTML version deleted]]