[BioC] arrayQualityMetrics error and question

[Wolfgang Huber]

Dear David

thanks. What's the output of 'sessionInfo()', and have you tried with an 
up-to-date version of arrayQualityMetrics?

http://www.bioconductor.org/packages/devel/bioc/html/arrayQualityMetrics.html 
or at least
http://www.bioconductor.org/packages/release/bioc/html/arrayQualityMetrics.html 


Let me know if the problem persists.

	Best wishes
	Wolfgang

Mar/4/12 11:02 AM, David Westergaard scripsit::
> 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
>
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-- 
Best wishes
	Wolfgang

Wolfgang Huber
EMBL
http://www.embl.de/research/units/genome_biology/huber