[BioC] arrayQualityMetrics is not working

[Wolfgang Huber]

Dear Núria

thank you for the feedback! You have (at least) two options:

1. as Steve already said, get access to an R for which the 'svg' device 
is available (this is easy on Linux, but might be fiddly on Windows), or

2. install the Cairo package from CRAN,
http://cran.r-project.org/web/packages/Cairo/index.html
and then the development version of arrayQualityMetrics
http://www.bioconductor.org/help/bioc-views/devel/bioc/html/arrayQualityMetrics.html
One way to do this is to download the .zip files and then in R, choose 
the "Packages" menu and do "Install package from local zip file".

The qualifications mentioned previously still apply:
https://stat.ethz.ch/pipermail/bioconductor/2011-February/037779.html


	Thanks and best wishes
	Wolfgang



nqueralt at clinic.ub.es scripsit 14/02/11 11:09:
> Dear all,
>
>
>
> I'm trying to run the arrayQualityMetrics function for the first time and an error comes out:
>
>
>
>> arrayQualityMetrics(RG, outdir="QCMetrics_onRG/", force=TRUE, do.logtransform=TRUE)
>
> The directory 'QCMetrics_onRG/' has been created.
>
> KernSmooth 2.23 loaded
>
> Copyright M. P. Wand 1997-2009
>
> (loaded the KernSmooth namespace)
>
> [[1]]
>
>
>
> Error en aqm.report.qm(p, obj[[i]], i, names(obj)[i]) :
>
>    no se pudo encontrar la función "svg"
>
> Además: Mensajes de aviso perdidos
>
> 1: The argument 'grouprep' of the function 'arrayQualityMetrics' is deprecated and will be ignored. Use 'intgroup' instead.
>
> 2: In dir.create(outdir, recursive = TRUE) :
>
>    'QCMetrics_onRG' already exists
>
>
>
> Here it is the traceback():
>
>
>
>> traceback()
>
> 7: aqm.report.qm(p, obj[[i]], i, names(obj)[i])
>
> 6: aqm.writereport(reporttitle, expressionset, obj)
>
> 5: arrayQualityMetrics(expressionset, outdir, force, do.logtransform,
>
>         intgroup, spatial)
>
> 4: arrayQualityMetrics(expressionset, outdir, force, do.logtransform,
>
>         intgroup, spatial)
>
> 3: .local(expressionset, outdir, force, do.logtransform, intgroup,
>
>         spatial)
>
> 2: arrayQualityMetrics(RG, outdir = "QCMetrics_onRG_1/", force = TRUE,
>
>         do.logtransform = TRUE)
>
> 1: arrayQualityMetrics(RG, outdir = "QCMetrics_onRG_1/", force = TRUE,
>
>         do.logtransform = TRUE)
>
>
>
> and the sessionInfo():
>
>
>
>> sessionInfo()
>
> R version 2.12.1 (2010-12-16)
>
> Platform: i386-pc-mingw32/i386 (32-bit)
>
>
>
> locale:
>
> [1] LC_COLLATE=Spanish_Spain.1252  LC_CTYPE=Spanish_Spain.1252    LC_MONETARY=Spanish_Spain.1252 LC_NUMERIC=C
>
> [5] LC_TIME=Spanish_Spain.1252
>
>
>
> attached base packages:
>
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
>
>
> other attached packages:
>
> [1] arrayQualityMetrics_3.2.4 vsn_3.18.0                affyPLM_1.26.0            preprocessCore_1.12.0     gcrma_2.22.0
>
> [6] affy_1.28.0               Biobase_2.10.0
>
>
>
> loaded via a namespace (and not attached):
>
>   [1] affyio_1.18.0        annotate_1.28.0      AnnotationDbi_1.12.0 beadarray_2.0.3      Biostrings_2.18.2    Cairo_1.4-6          DBI_0.2-5
>
>   [8] genefilter_1.32.0    grid_2.12.1          hwriter_1.3          IRanges_1.8.8        KernSmooth_2.23-4    lattice_0.19-17      latticeExtra_0.6-14
>
> [15] limma_3.6.9          marray_1.28.0        RColorBrewer_1.0-2   RSQLite_0.9-4        simpleaffy_2.26.1    splines_2.12.1       stats4_2.12.1
>
> [22] survival_2.36-2      SVGAnnotation_0.7-2  tools_2.12.1         XML_3.2-0.2          xtable_1.5-6
>
>
>
> Anyone knows how could I fix it? Many thanks in advance!
>
>
>
> Best regards,
>
>
>
> Núria
>
>
>
>
> 	[[alternative HTML version deleted]]
>
>
>
>
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-- 


Wolfgang Huber
EMBL
http://www.embl.de/research/units/genome_biology/huber