Thanks Jean, Here is what I got by adding antialias="default". Hope it helps you fix it. > maQualityPlots(mraw,antialias="default") Error in baseViewports() : could not find function "viewport" > library(gridBase) Loading required package: grid > maQualityPlots(mraw,antialias="default") Error in as.double(y) : cannot coerce type 'S4' to vector of type 'double' Tim Cam > CC: bioconductor@r-project.org; tim_cam2010@live.com > From: jean.yang@sydney.edu.au > Subject: Re: [BioC] Marray Quality Check > Date: Fri, 17 Aug 2012 11:33:00 +1000 > To: guest@bioconductor.org > > Hi Tim, > > I might need to fix a few defaults, but can you see if adding > > antialias="default" > > In the argument of maQualityPlots will work or not. I will test out the package later today to make sure it runs. > > Jean > > Sent from my iPhone > > On 17/08/2012, at 0:08, "Tim Cam [guest]" <guest@bioconductor.org> wrote: > > > > > Hi All, > > > > Just go through the quality check for the marrays and I am a newbie. The function maQualityPlots seems not working. Just ask what kind of problem it is? The R code is listed below: > > > > Thanks, > > > > Tim Cam > > > >> library(beta7) > >> library(arrayQuality) > >> datadir <- system.file("beta7",package="beta7") > >> TargetInfo <- read.marrayInfo(file.path(datadir,"TargetBeta7.txt")) > >> mraw <- read.GenePix(targets=TargetInfo) > > Reading ... 6Hs.195.1.gpr > > Reading ... 6Hs.168.gpr > > Reading ... 6Hs.166.gpr > > Reading ... 6Hs.187.1.gpr > > Reading ... 6Hs.194.gpr > > Reading ... 6Hs.243.1.gpr > >> maQualityPlots(mraw) > > Error in match.arg(antialias, aa.win) : 'arg' must be of length 1 > >> maQualityPlots(mraw,DEBUG=TRUE) > > [1] "function starting" > > [1] 23184 6 > > [1] "Re-evaluate Weight" > > check Control color code 2 3 4 5 6 > > [1] "Set up data and normalization" > > [1] "Reading normalization parameters" > > list() > > Using normalization method: p > > [1] "Name the output file" > > [1] "6Hs.195.1" > > [1] "Name of output device" > > [1] "diagPlot.6Hs.195.1.png" > > [1] "start layout" > > Error in match.arg(antialias, aa.win) : 'arg' must be of length 1 > >> > > > > > > -- output of sessionInfo(): > > > >> sessionInfo() > > R version 2.15.0 (2012-03-30) > > Platform: i386-pc-mingw32/i386 (32-bit) > > > > locale: > > [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 LC_MONETARY=English_United States.1252 > > [4] LC_NUMERIC=C LC_TIME=English_United States.1252 > > > > attached base packages: > > [1] stats graphics grDevices utils datasets methods base > > > > other attached packages: > > [1] arrayQuality_1.34.0 beta7_1.0.3 marray_1.34.0 limma_3.12.1 AmpAffyExample_1.2.10 simpleaffy_2.32.0 > > [7] genefilter_1.38.0 RColorBrewer_1.0-5 hgu133bcdf_2.10.0 ALLMLL_1.2.12 affycomp_1.32.0 hgu95av2probe_2.10.0 > > [13] affypdnn_1.30.0 affyPLM_1.32.0 preprocessCore_1.18.0 gcrma_2.28.0 hgu95av2cdf_2.10.0 hgu133acdf_2.10.0 > > [19] AnnotationDbi_1.18.1 affydata_1.11.16 BiocInstaller_1.4.7 affy_1.34.0 Biobase_2.16.0 BiocGenerics_0.2.0 > > > > loaded via a namespace (and not attached): > > [1] affyio_1.24.0 annotate_1.34.1 Biostrings_2.24.1 DBI_0.2-5 grid_2.15.0 gridBase_0.4-5 hexbin_1.26.0 > > [8] IRanges_1.14.4 lattice_0.20-6 RSQLite_0.11.1 splines_2.15.0 stats4_2.15.0 survival_2.36-14 tools_2.15.0 > > [15] XML_3.9-4.1 xtable_1.7-0 zlibbioc_1.2.0 > > > > -- > > Sent via the guest posting facility at bioconductor.org. > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@r-project.org > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor [[alternative HTML version deleted]]