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

 


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