[BioC] arrayQualityMetrics error and question
David Westergaard
david at harsk.dk
Mon Mar 5 23:04:36 CET 2012
Hi,
It seems to be working now, with arrayQualityMetrics v3.10. The only
"problem" is, I am getting alot of warnings, more than 50.
All of them are:
In grid.Call.graphics(L_segments, x$x0, x$y0, x$x1, x$y1, ... :
X11 protocol error: BadMatch (invalid parameter attributes)
Can I just disregard these? Reports are still being produced.
Also, have methods changed from arrayQualityMetrics 2.6.0 -> 3.10?
Some arrays which previously did not pass some tests, not pass the
tests. And vice versa.
For instance, in version 2.6.0, using data from
http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-2261, 2 arrays
failed 1 test (p0742_O11_120_24.CEL and p0742_O3_000_11.CEL), 1 array
failed 2 tests (p0742_O3_120_12.CEL), and 1 array failed 3 tests
(p0742_O15_120_40.CEL
In version 3.10, 1 array failed 1 test (p0742_O3_120_12.CEL) and 1
array failed 2 tests (p0742_O15_120_40.CEL).
Sessioninfo:
> sessionInfo()
R version 2.14.1 (2011-12-22)
Platform: ia64-unknown-linux-gnu (64-bit)
locale:
[1] C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] nugohs1a520180cdf_2.4.1 hgu133plus2cdf_2.9.1
[3] AnnotationDbi_1.16.18 affy_1.32.1
[5] Biobase_2.14.0 arrayQualityMetrics_3.10.0
loaded via a namespace (and not attached):
[1] BiocInstaller_1.2.1 Biostrings_2.22.0 Cairo_1.5-1
[4] DBI_0.2-5 Hmisc_3.9-2 IRanges_1.12.6
[7] KernSmooth_2.23-7 RColorBrewer_1.0-5 RSQLite_0.11.1
[10] SVGAnnotation_0.93-1 XML_3.9-4 affyPLM_1.30.0
[13] affyio_1.22.0 annotate_1.32.1 beadarray_2.4.1
[16] cluster_1.14.2 genefilter_1.36.0 grid_2.14.1
[19] hwriter_1.3 lattice_0.20-0 latticeExtra_0.6-19
[22] limma_3.10.3 preprocessCore_1.16.0 setRNG_2009.11-1
[25] splines_2.14.1 survival_2.36-12 tools_2.14.1
[28] vsn_3.22.0 xtable_1.7-0 zlibbioc_1.0.1
Best,
David
2012/3/5 David Westergaard <david at harsk.dk>:
> 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
>>>>>
>>>>> _______________________________________________
>>>>> Bioconductor mailing list
>>>>> Bioconductor at r-project.org
>>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>>>>> Search the archives:
>>>>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>>>>
>>>>
>>>>
>>>> --
>>>> Best wishes
>>>> Wolfgang
>>>>
>>>> Wolfgang Huber
>>>> EMBL
>>>> http://www.embl.de/research/units/genome_biology/huber
>>>>
>>>> _______________________________________________
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>>>
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