[BioC] Marray Quality Check

[Jean Yang]

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 at 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  
> 
> --
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> 
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