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 [[alternative HTML version deleted]]

On 09/17/2011 01:44 AM, Ignacio Lopez De Ullibarri Galparsoro wrote: > > > > > > 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 ... Thanks Ignacio I updated this in the 'devel' branch of Bioconductor, available with the devel version of R. Look for package version 1.31.1 in the next couple of days. This package has not been actively maintained for several release cycles, and there are a number of suspicious 'notes' when run through R CMD check. arrayQualityMetrics is very actively maintained. I recommend that you use arrayQualityMetrics instead, even if it does not provide exactly the same functionality. Martin > > 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 > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- Computational Biology Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: M1-B861 Telephone: 206 667-2793