Hello, I've been trying to generate qualitative QC plots on a two-color set of arrays using arrayQuality. When I first generated the error I tried using the swirl dataset to see if it was a problem with my data. The error still came up. It seems that the dev switch is being set twice. I also tried setting dev='png'/'pdf' etc., but still the same error. I looked through the source of arrayQuality and I can't find any unclosed quotes that may generate this error, but I could be wrong. Any ideas? ============ > list.files() [1] "fish.gal" "SpotTypes.txt" "swirl.1.spot" "swirl.2.spot" "swirl.3.spot" "swirl.4.spot" "SwirlSample.txt" > targets<-readTargets('SwirlSample.txt') > RG<-read.maimages(targets,source='spot') Read swirl.1.spot Read swirl.2.spot Read swirl.3.spot Read swirl.4.spot > RG$genes<-readGAL('fish.gal') > RG$printer<-getLayout(RG$genes) > maQualityPlots(RG) Error: duplicate switch defaults: 'list(dev =...' and '' > sessionInfo() R version 2.13.0 (2011-04-13) Platform: i386-pc-mingw32/i386 (32-bit) locale: [1] LC_COLLATE=English_United Kingdom.1252 LC_CTYPE=English_United Kingdom.1252 LC_MONETARY=English_United Kingdom.1252 LC_NUMERIC=C [5] LC_TIME=English_United Kingdom.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] arrayQuality_1.30.0 convert_1.28.0 marray_1.30.0 limma_3.8.1 Biobase_2.12.1 loaded via a namespace (and not attached): [1] grid_2.13.0 gridBase_0.4-3 hexbin_1.26.0 lattice_0.19-23 RColorBrewer_1.0-2 tools_2.13.0 ================= Kind regards, Fabio Liberante