[BioC] problem with arrayQualityMetrics

Joern Toedling Joern.Toedling at curie.fr
Wed Nov 25 11:43:18 CET 2009


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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