[BioC] arrayQualityMetrics error and question

[David Westergaard]

Hello,

I am trying to use the BioC package arrayQualityMetrics to asses the
quality of a range of experiments. I am, however, running into errors,
when processing Affymetrix Hugene designs, particularly
http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-33443

I'm using the following code:

library('arrayQualityMetrics'); library('affy')
mixture.batch <- ReadAffy()
arrayQualityMetrics(expressionset=mixture.batch,
	outdir=paste("/home/projects/rgroups/cheminf/dwe/figures/self_processed/QA/",veggie[i],sep=""),
	do.logtransform=TRUE,
	force=TRUE
)

And get the error:

Error in setQCEnvironment(cdfn) :
  Could not find array definition file ' hugene10stv1cdf.qcdef '.
Simpleaffy does not know the QC parameters for this array type.
See the package vignette for details about how to specify QC
parameters manually.

Error in density.default(as.matrix(log2(mm(expressionset))), ...) :
  'x' contains missing values
In addition: Warning message:
In aqm.qcstats(expressionset) :
  'plot(qcStats)' from the package 'simpleaffy' failed for this dataset.
Error in obj[[i]]$legend : $ operator is invalid for atomic vectors
In addition: Warning message:
In arrayQualityMetrics(expressionset = mixture.batch, outdir =
paste("/home/projects/rgroups/cheminf/dwe/figures/self_processed/QA/",
 :
  Cannot draw the Perfect Match versus MisMatch plot


Now, from what I've read in an older mail to this list, Hugene is a
PM-only type design, building my own .qcdef wouldn't really do no
good. Googling around didn't really give any useful information. So
how do I get by this problem?

Also, why do only some array types output a complete index.html,
providing the numbers for outlier detection?

Best Regards,
David Westergaard