[BioC] arrayQualityMetrics error and question
Daniel Aaen Hansen
daniel at intomics.com
Wed Mar 7 11:23:32 CET 2012
Dear Wolfgang and David,
I also get more than 50 warnings when I use arrayQualityMetrics. Most of the warnings are of the type:
1: In grid.Call.graphics(L_rect, x$x, x$y, x$width, x$height, ... :
X11 protocol error: BadMatch (invalid parameter attributes)
But there are also some others (two of each):
27: In plot.xy(xy, type, ...) :
X11 protocol error: BadMatch (invalid parameter attributes)
29: In axis(side = side, at = at, labels = labels, ...) :
X11 protocol error: BadMatch (invalid parameter attributes)
31: In box(...) : X11 protocol error: BadMatch (invalid parameter attributes)
33: In title(...) : X11 protocol error: BadMatch (invalid parameter attributes)
35: In segments(x0 = x0[wh] + dx, x1 = x1[wh] - dx, y0 = y[wh], ... :
X11 protocol error: BadMatch (invalid parameter attributes)
37: In int_abline(a = a, b = b, h = h, v = v, untf = untf, ... :
X11 protocol error: BadMatch (invalid parameter attributes)
39: In text.default(par("usr")[1], y, paste(rev(y)), adj = c(1, ... :
X11 protocol error: BadMatch (invalid parameter attributes)
There is also an error in the generated HTML report. The principal component analysis in figure 3 is static - making it more or less useless because you can't see which dots corresponds to which arrays. The following error message is printed in the report:
Note: the figure is static - enhancement with interactive effects failed. This is either due to a version incompatibility of the 'SVGAnnotation' R package and your version of 'Cairo' or 'libcairo', or due to plot misformating. Please consult the Bioconductor mailing list, or contact the maintainer of 'arrayQualityMetrics' with a reproducible example in order to fix this problem.
Could this error in the report be related to the warnings I get? I use the following commands to reproduce the problem:
library(affy)
library(arrayQualityMetrics)
data = ReadAffy()
arrayQualityMetrics(expressionset=data, outdir="test", force=TRUE, do.logtransform=TRUE)
In addition, I noted that if I load 'arrayQualityMetrics' before 'affy', I get two messages that I don't get if I load 'affy' first:
> library(arrayQualityMetrics)
Creating a generic function for ‘boxplot’ from package ‘graphics’ in package ‘affyPLM’
Creating a generic function for ‘hist’ from package ‘graphics’ in package ‘affyPLM’
> library(affy)
My R installation is as follows:
R version 2.14.2
arrayQualityMetrics version 3.10.0
affyPLM version 1.30.0
Cairo version 1.5-1
SVGAnnotation version 0.9-0
And on the system we run:
libcairo2 version 1.8.10
sessionInfo() contains:
> sessionInfo()
R version 2.14.2 (2012-02-29)
Platform: x86_64-unknown-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=en_DK.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_DK.UTF-8 LC_COLLATE=en_DK.UTF-8
[5] LC_MONETARY=en_DK.UTF-8 LC_MESSAGES=en_DK.UTF-8
[7] LC_PAPER=C LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_DK.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] hgu133acdf_2.9.1 AnnotationDbi_1.16.18
[3] arrayQualityMetrics_3.10.0 affy_1.32.1
[5] Biobase_2.14.0
loaded via a namespace (and not attached):
[1] affyio_1.22.0 affyPLM_1.30.0 annotate_1.32.1
[4] beadarray_2.4.1 BiocInstaller_1.2.1 Biostrings_2.22.0
[7] Cairo_1.5-1 cluster_1.14.2 DBI_0.2-5
[10] genefilter_1.36.0 grid_2.14.2 Hmisc_3.9-2
[13] hwriter_1.3 IRanges_1.12.6 KernSmooth_2.23-7
[16] lattice_0.20-0 latticeExtra_0.6-19 limma_3.10.2
[19] preprocessCore_1.16.0 RColorBrewer_1.0-5 RSQLite_0.11.1
[22] setRNG_2009.11-1 splines_2.14.2 survival_2.36-12
[25] SVGAnnotation_0.9-0 tools_2.14.2 vsn_3.22.0
[28] XML_3.9-4 xtable_1.7-0 zlibbioc_1.0.0
Best regards,
Daniel
On Mar 7, 2012, at 10:37 AM, David Westergaard wrote:
> 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
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> 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
>>>>>>
>>>>>>
>>>>>> _______________________________________________
>>>>>> 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
>>>
>>>
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>>> Bioconductor mailing list
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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
>> Search the archives:
>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>
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