
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.
> > 
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