[BioC] arrayQuality - maQualityPlots - Error: duplicate switch defaults: 'list(dev =...' and ''

Fabio Liberante fabio.liberante at gmail.com
Tue Jun 7 16:12:22 CEST 2011


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"
> 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)

[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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