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/arrayQu alityMetrics.html >>>>>>>>> or at least >>>>>>>>> >>>>>>>>> http://www.bioconductor.org/packages/release/bioc/html/array QualityMetrics.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/s elf_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 > > [[alternative HTML version deleted]]