[BioC] arrayQualityMetrics error and question

[Dan Tenenbaum]

Hi,

On Sun, Mar 4, 2012 at 2:44 PM, David Westergaard <david at harsk.dk> wrote:
> 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)

R 2.14 is >= R 2.13, so beadarray works on R-2.14.
What is the specific error message (and sessionInfo()) you get when
trying to install arrayQualityMetrics (or beadarray) on R 2.14?

Dan


> 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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>>
>>
>>
>> --
>> Best wishes
>>        Wolfgang
>>
>> Wolfgang Huber
>> EMBL
>> http://www.embl.de/research/units/genome_biology/huber
>>
>> _______________________________________________
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>
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