[BioC] arrayQualityMetrics error and question

David Westergaard david at harsk.dk
Wed Mar 7 10:37:45 CET 2012


Dear Wolfgang,

I think that it may be a slighty broken Cairo installed in my homedir.
Sadly, our Cairo graphics installation at the institute is quite old,
version 1.0. arrayQualityMetrics depends on the R package Cairo which
depends on a Cairo graphics installation >= 1.2. I think I may the
installation to my homedir is lacking something, but I cannot figure
out what from either the INSTALL document, or the Cairo graphics
documentation.
Also, looking through warnings(), I notice a new warning:

Error in UseMethod("xmlAttrs", node) :
  no applicable method for 'xmlAttrs' applied to an object of class "NULL"

Might this also be due to a partially broken cairo graphics installation?

On another note, about X11 - Is it possible to not have PNGs produced?
I currently have to run my scripts on a remote server due to memory
issues, and since PNG requires a X11 forward, it is difficult to leave
the scripts running over the night. Or is there another, and better,
solution?

I also have a question about outlier detection. I am not interested in
a thorough description of the algorithm, but I would like an idea of
how the threshold for Outlier detection for Distances between array is
determined. The HTML just states "Exceptionally large". I haven't been
able to find anything about this in either the Introduction, or
Advanced Topics manual, nor in ?outliers.

Best regards,
David

2012/3/6 Wolfgang Huber <whuber at embl.de>:
> Dear David
>
> Mar/5/12 11:04 PM, David Westergaard scripsit::
>
>> 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.
>
>
> I have never seen these before. It might be a problem specific to your
> (slightly broken?) R installation.
>
>
>> 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.
>
>
> Yes. Hence the different major version number. The new methods for outlier
> detection are documented in the report - please let me know if you have
> questions or comments about these.
>
> Of course, outlier detection is a poorly defined question, and there is no
> 'right' or 'wrong' answer. These are hints which are intended to be followed
> up manually. If you want to automate outlier detection, you need to limit
> the scope to a particular platform and experimental design, and then choose
> and calibrate the metrics used. I have added an extra note to this effect to
> the introduction of the report.
>
>        Best wishes
>        Wolfgang
>
>
>> 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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>>
>>
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>
>
>
> --
> Best wishes
>        Wolfgang
>
> Wolfgang Huber
> EMBL
> http://www.embl.de/research/units/genome_biology/huber
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioconductor
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