[BioC] arrayQualityMetrics and NChannelSets

[Tim Rayner]

Hi,

Just a quick note to observe that the current stable version of
arrayQualityMetrics seems to have a problem with NChannelSet objects:

> nc
NChannelSet (storageMode: lockedEnvironment)
assayData: 1178100 features, 50 samples
  element names: exprs
protocolData
  rowNames: GWAS16.10_160_CD16.CEL GWAS16.11_158_CD16.CEL ...
    GWAS16.L_148_CD16.CEL (50 total)
  varLabels: exprs dates
  varMetadata: labelDescription channel
phenoData
  rowNames: GWAS16.10_160_CD16.CEL GWAS16.11_158_CD16.CEL ...
    GWAS16.L_148_CD16.CEL (50 total)
  varLabels: info.batch.name operator ... visual_check (62 total)
  varMetadata: labelDescription channel
featureData: none
experimentData: use 'experimentData(object)'
Annotation: pd.hugene.1.1.st.v1


> arrayQualityMetrics(nc)
The directory 'arrayQualityMetrics report for nc' has been created.
Error in rep("#1F78B4", x$numArrays) : invalid 'times' argument


> traceback()
4: intgroupColors(x)
3: append(x, intgroupColors(x))
2: prepdata(expressionset, intgroup = intgroup, do.logtransform =
do.logtransform)
1: arrayQualityMetrics(nc)


> validObject(nc)
[1] TRUE


> sessionInfo()
R version 2.13.1 (2011-07-08)
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)

locale:
[1] en_GB.UTF-8/en_GB.UTF-8/C/C/en_GB.UTF-8/en_GB.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
 [1] arrayQualityMetrics_3.8.0 pd.hugene.1.1.st.v1_3.2.0
 [3] oligo_1.16.0              preprocessCore_1.14.0
 [5] oligoClasses_1.14.0       RSQLite_0.9-4
 [7] DBI_0.2-5                 ClinStudyWeb_0.2.4
 [9] rjson_0.2.5               SmithLabArray_0.5.5
[11] limma_3.8.3               Biobase_2.12.2

loaded via a namespace (and not attached):
 [1] affxparser_1.24.0    affy_1.30.0          affyio_1.20.0
 [4] affyPLM_1.28.5       annotate_1.30.1      AnnotationDbi_1.14.1
 [7] beadarray_2.2.0      Biostrings_2.20.3    bit_1.1-7
[10] Cairo_1.4-9          cluster_1.14.0       ff_2.2-3
[13] gdata_2.8.1          genefilter_1.34.0    gplots_2.10.1
[16] grid_2.13.1          gtools_2.6.2         Hmisc_3.8-3
[19] hopach_2.12.0        hwriter_1.3          IRanges_1.10.6
[22] lattice_0.19-33      latticeExtra_0.6-18  RColorBrewer_1.0-5
[25] RCurl_1.6-10         setRNG_2009.11-1     splines_2.13.1
[28] survival_2.36-9      SVGAnnotation_0.9-0  tcltk_2.13.1
[31] tools_2.13.1         vsn_3.20.0           XML_3.4-3
[34] xtable_1.5-6

Given that the documentation claims to support such objects I'm
assuming this is a bug? I'm currently coercing GeneFeatureSet objects
to NChannelSet and as you can see the conversion yields valid objects.
As a workaround, is there an alternative class to which I should be
coercing?

Many thanks,

Tim Rayner

-- 
Bioinformatician
Smith Lab, CIMR
University of Cambridge