




There is a bug in the following code chunk of maQualityPlots(): 

plotdef <- switch(dev, bmp = list(dev = list(width = 1600, height = 1200, bg = "white"), suffix = "bmp"), 
jpeg = list(dev = list(quality = 100, width = 1600, height = 1200, bg = "white"), suffix = "jpeg"), 
postscript = list(dev = list(bg = "white"), suffix = "ps"), 
png = list(dev = list(width = 1600, height = 1200, bg = "white"), suffix = "png"), 
list(dev = list(width = 1600, height = 1200, bg = "white"), suffix = "png"), ) 

In relation with the syntax of the '...' argument of switch, one can read from the online help (?switch): "If there is more than one such argument an error is returned. Before R 2.13.0 the first one would have been used". 

So, this problem should be easily fixed by deleting the ',' immediately before the closing ')'. 

But I am asking myself if this function does not have in fact some further problems ... 

Ignacio L. de Ullibarri 


On Tue, Jun 7, 2011 at 16:12:22, Fabio Liberante < fabio.liberante at gmail.com > wrote: 
> 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 


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