[BioC] problem with arrayQualityMetrics

[Audrey Kauffmann]

Hi Joern,

Thank you for your feedback. You are using the development version 2.5.2
and I have recently added legend on the RNA Degradation plot of this
version, apparently I need to correct it.

The release version 2.4.2 should not have this problem.

Best wishes,
Audrey




> Hello,
>
> I think there may be a problem with the current version of
> arrayQualityMetrics. I have downloaded two CEL files from GEO, read them
> into
> an AffyBatch object using the function ReadAffy. The object looks good to
> me.
>
>> AB.Endoh
> AffyBatch object
> size of arrays=1002x1002 features (17 kb)
> cdf=Mouse430_2 (45101 affyids)
> number of samples=2
> number of genes=45101
> annotation=mouse4302
>
> When I now call arrayQualityMetrics on this object, no result files are
> produced and I receive the following errors:
>
>> arrayQualityMetrics(AB.Endoh, outdir="aqm_raw", do.logtransform=TRUE)
> The directory 'aqm_raw' has been created.
> Error in `sampleNames<-`(`*tmp*`, value = NULL) :
>   number of new names (0) should equal number of rows in
> AnnotatedDataFrame (2)
> Error in obj[[i]]$legend : $ operator is invalid for atomic vectors
> In addition: Warning message:
> In arrayQualityMetrics(AB.Endoh, outdir = "aqm_raw", do.logtransform =
> TRUE) :
>   Cannot draw the RNA degradation plot
>
> However, creating the RNA degradation plot and other plots by hand works
> well.
> For example,
>
>> D <- AffyRNAdeg(AB.Endoh)
>> plotAffyRNAdeg(D)
>
> gives the correct plot.
>
> So it looks like there is a problem with arrayQualityMetrics.
>
> My sessionInfo output is:
>
>> sessionInfo()
> R version 2.11.0 Under development (unstable) (2009-10-27 r50222)
> x86_64-unknown-linux-gnu
>
> attached base packages:
> [1] stats     graphics  grDevices datasets  utils     methods   base
>
> other attached packages:
>  [1] mouse4302cdf_2.5.0           org.Mm.eg.db_2.3.6
>  [3] RSQLite_0.7-3                DBI_0.2-4
>  [5] AnnotationDbi_1.9.2          biomaRt_2.3.0
>  [7] arrayQualityMetrics_2.5.2    affyPLM_1.23.0
>  [9] preprocessCore_1.9.0         gcrma_2.19.0
> [11] mouse4302mmentrezgcdf_12.0.0 vsn_3.15.0
> [13] affy_1.25.2                  Biobase_2.7.0
>
> loaded via a namespace (and not attached):
>  [1] affyio_1.15.1      annotate_1.25.0    beadarray_1.15.0
> Biostrings_2.15.6
>  [5] genefilter_1.29.2  grid_2.11.0        hwriter_1.1
> IRanges_1.5.6
>  [9] lattice_0.17-26    latticeExtra_0.6-4 limma_3.3.1
> marray_1.25.0
> [13] RColorBrewer_1.0-2 RCurl_1.3-0        simpleaffy_2.23.0
> splines_2.11.0
> [17] stats4_2.11.0      survival_2.35-7    tools_2.11.0       XML_2.6-0
> [21] xtable_1.5-6
>
>
> ---
> Joern Toedling
> Institut Curie -- U900
> 26 rue d'Ulm, 75005 Paris, FRANCE
> Tel. +33 (0)156246927
>
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