Dear Wolfgang,

Thanks for your reply. We updated our cairo graphics library to version 1.10.2 and that solved the problem with the PCA plot such that it is now interactive. I still get all the warnings and the different behavior depending on whether 'affy' or 'arrayQualityMetrics' is loaded first (described below), but if it is not serious, I can live with that.

Best,
Daniel


On Mar 7, 2012, at 3:04 PM, Wolfgang Huber wrote:

> 
> Dear Daniel
> 
> thanks. Maybe you need to get in touch with a system administration expert to troubleshoot your installation of R.
> 
> I would recommend they update your cairo graphics library. E.g. on my system I get
> $ pkg-config --modversion cairo
> 1.10.2
> and that works well. Version 1.8.10, which you say you use, is over two years old. You would be  ()on your own with that.
> 
> 	Best wishes
> 	Wolfgang
> 
> 
> 
> Daniel Aaen Hansen scripsit 03/07/2012 11:23 AM:
>> 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@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@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@fhcrc.org>:
>>>>>>> 
>>>>>>> Hi,
>>>>>>> 
>>>>>>> On Sun, Mar 4, 2012 at 2:44 PM, David Westergaard<david@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@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@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@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@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@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@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@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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