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 [[alternative HTML version deleted]]