[BioC] arrayQualityMetrics::aqm.nuse and GeneST

[Tim Rayner]

Hi,

I think I've run into a bug on the latest arrayQualityMetrics release.
I'm running the function on an AffyBatch object created from HuGene ST
1.0 CEL files which I've tested with previous versions of
arrayQualityMetrics without any problems:

> arrayQualityMetrics(cd8, outdir='canonical_qc')
The directory 'canonical_qc' has been created.
Error in quantile.default(dataprep$dat[ss, ], probs = 0.01) :
  missing values and NaN's not allowed if 'na.rm' is FALSE
Error in density.default(as.matrix(log2(mm(expressionset))), ...) :
  'x' contains missing values
In addition: Warning message:
In nuse$legend = paste(phrase$fig("Normalized Unscaled Standard Error
(NUSE)"),  :
  Coercing LHS to a list

It appears that the aqm.nuse() function is throwing the error. The
error does not occur if I use CELs from the HG-U133A platform, so I'm
guessing that it's a problem running the function on CELs from the
PM-only Gene ST platform?

Aside from that, thank you very much for the improvements with this
release; the new QC plots very useful indeed.

Best regards,

Tim Rayner



sessionInfo() follows:

R version 2.12.0 (2010-10-15)
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] tcltk     stats     graphics  grDevices utils     datasets  methods
[8] base

other attached packages:
 [1] Rmpi_0.5-8                affyPara_1.10.0
 [3] aplpack_1.2.3             snow_0.3-3
 [5] hugene10stv1cdf_3.24.1    arrayQualityMetrics_3.2.0
 [7] affyPLM_1.26.0            preprocessCore_1.12.0
 [9] gcrma_2.22.0              affy_1.28.0
[11] vsn_3.18.0                Biobase_2.10.0

loaded via a namespace (and not attached):
 [1] affyio_1.18.0        annotate_1.28.0      AnnotationDbi_1.12.0
 [4] beadarray_2.0.1      Biostrings_2.18.0    DBI_0.2-5
 [7] genefilter_1.32.0    grid_2.12.0          hwriter_1.2
[10] IRanges_1.8.2        lattice_0.19-13      latticeExtra_0.6-14
[13] limma_3.6.6          marray_1.28.0        RColorBrewer_1.0-2
[16] RSQLite_0.9-3        simpleaffy_2.26.0    splines_2.12.0
[19] stats4_2.12.0        survival_2.36-1      SVGAnnotation_0.6-0
[22] tools_2.12.0         XML_3.2-0            xtable_1.5-6


-- 
Tim Rayner
Bioinformatician, Smith Lab
CIMR, University of Cambridge, U.K.