[BioC] arrayQualityMetrics error and question

Mon Mar 5 00:13:57 CET 2012

Hi,

I did not express myself clearly enough - I actually didn't have
trouble with beadarray. The package giving me trouble was Cairo, but I
solved that by installing newest cairoDevice pacakge, followed by
Cairo-1.4-5. I'm now running R-2.14 with arrayQualityMetrics v3.10 -
I'll let you know if I encounter any problems.

Best,
David

2012/3/4 Dan Tenenbaum <dtenenba at fhcrc.org>:
> 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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