Hello,

I am new to R and Bioconductor. When going through the tutorial for marray, I ran out on a problem with maQualityPlots function. The plots are not displayed (only single MA Raw plot when argument save = F). I tried both beta7 and swirl datasets with the same result. What could cause the problem?
Thanks,

Vojta Pavlik

library(marray)
Loading required package: limma
> data(swirl)
> dir(system.file("swirldata",package="marray"))
[1] "fish.gal"        "swirl.1.spot"    "swirl.2.spot"    "swirl.3.spot"    "swirl.4.spot"
[6] "SwirlSample.txt"
> datadir <- system.file("swirldata",package="marray")
> swirlTargets <-  read.marrayInfo(file.path(datadir,"SwirlSample.txt"))
> mraw = read.Spot(targets=swirlTargets,path=datadir)
Reading ...  \\R/R-2.15.2 reinstal/library/marray/swirldata/swirl.1.spot
Reading ...  \\R/R-2.15.2 reinstal/library/marray/swirldata/swirl.2.spot
Reading ...  \\R/R-2.15.2 reinstal/library/marray/swirldata/swirl.3.spot
Reading ...  \\R/R-2.15.2 reinstal/library/marray/swirldata/swirl.4.spot
> galinfo <-  read.Galfile("fish.gal",path=datadir)
> library(arrayQuality)
> maQualityPlots(mraw)
Error in match.arg(antialias, aa.win) : 'arg' must be of length 1
> maQualityPlots(mraw, save=F)
Error in as.double(y) :
  cannot coerce type 'S4' to vector of type 'double'
#a single MA Plot is generated


> sessionInfo()
R version 2.15.2 (2012-10-26)
Platform: i386-w64-mingw32/i386 (32-bit)

locale:
[1] LC_COLLATE=Czech_Czech Republic.1250  LC_CTYPE=Czech_Czech Republic.1250
[3] LC_MONETARY=Czech_Czech Republic.1250 LC_NUMERIC=C
[5] LC_TIME=Czech_Czech Republic.1250

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] arrayQuality_1.36.0 marray_1.36.0       limma_3.14.4

loaded via a namespace (and not attached):
[1] grid_2.15.2        gridBase_0.4-6     hexbin_1.26.0      lattice_0.20-13
[5] RColorBrewer_1.0-5 tools_2.15.2


















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