Hi Wolfgang,
The problem hasn't really resolved itself. I can't update any further,
since I'm having trouble installing arrayQualityMatrics with R-2.14 on
the server I have access to. (beadarray, which is a requirement, needs
R>=2.13) Cairo fails to install, giving two errors:
cairotalk.c:894: error: 'CAIRO_EXTEND_PAD' undeclared (first use in
this function)
cairotalk.c:322: error: 'CAIRO_SURFACE_TYPE_IMAGE' undeclared (first
use in this function)
I can install both fine on my own computer, however, but I do not have
enough memory to process the files myself. Are there any options
besides spatial=FALSE to reduce memory usage?
Here's the output of sessionInfo()
> sessionInfo()
R version 2.11.0 (2010-04-22)
ia64-unknown-linux-gnu
locale:
[1] C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] arrayQualityMetrics_2.6.0 affyPLM_1.24.1
[3] preprocessCore_1.10.0 gcrma_2.20.0
[5] affy_1.26.1 Biobase_2.8.0
loaded via a namespace (and not attached):
[1] AnnotationDbi_1.10.0 Biostrings_2.16.9 DBI_0.2-5
[4] IRanges_1.6.8 RColorBrewer_1.0-2 RSQLite_0.9-4
[7] affyio_1.16.0 annotate_1.26.0 beadarray_1.16.0
[10] genefilter_1.30.0 grid_2.11.0 hwriter_1.2
[13] lattice_0.18-5 latticeExtra_0.6-18 limma_3.4.5
[16] marray_1.26.0 simpleaffy_2.24.0 splines_2.11.0
[19] stats4_2.11.0 survival_2.35-8 tools_2.11.0
[22] vsn_3.16.0 xtable_1.5-6
Best,
David
2012/3/4 Wolfgang Huber <whuber at embl.de>:
> 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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>> Bioconductor at r-project.org
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>> Search the archives:
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>
>
>
> --
> Best wishes
> Wolfgang
>
> Wolfgang Huber
> EMBL
> http://www.embl.de/research/units/genome_biology/huber
>
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