Question: arrayQualityMetrics error and question
0
gravatar for David Westergaard
7.4 years ago by
David Westergaard280 wrote:
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
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ADD COMMENTlink modified 7.4 years ago by Wolfgang Huber13k • written 7.4 years ago by David Westergaard280
Answer: arrayQualityMetrics error and question
0
gravatar for Wolfgang Huber
7.4 years ago by
EMBL European Molecular Biology Laboratory
Wolfgang Huber13k wrote:
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/arrayQualityMetri cs.html or at least http://www.bioconductor.org/packages/release/bioc/html/arrayQualityMet rics.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
ADD COMMENTlink written 7.4 years ago by Wolfgang Huber13k
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) 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/arrayQualityMet rics.html > or at least > http://www.bioconductor.org/packages/release/bioc/html/arrayQualityM etrics.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_proc essed/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
ADD REPLYlink written 7.4 years ago by David Westergaard280
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/arrayQualityMe trics.html >> or at least >> http://www.bioconductor.org/packages/release/bioc/html/arrayQuality Metrics.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_pro cessed/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
ADD REPLYlink written 7.4 years ago by Dan Tenenbaum8.2k
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/arrayQualityM etrics.html >>> or at least >>> http://www.bioconductor.org/packages/release/bioc/html/arrayQualit yMetrics.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_pr ocessed/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
ADD REPLYlink written 7.4 years ago by David Westergaard280
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/arrayQuality Metrics.html >>>> or at least >>>> http://www.bioconductor.org/packages/release/bioc/html/arrayQuali tyMetrics.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_p rocessed/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
ADD REPLYlink written 7.4 years ago by David Westergaard280
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/arrayQualit yMetrics.html >>>>> or at least >>>>> http://www.bioconductor.org/packages/release/bioc/html/arrayQual ityMetrics.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 > > _______________________________________________ > 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
ADD REPLYlink written 7.4 years ago by Wolfgang Huber13k
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/arrayQuali tyMetrics.html >>>>>> or at least >>>>>> >>>>>> http://www.bioconductor.org/packages/release/bioc/html/arrayQua lityMetrics.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 >> >> >> _______________________________________________ >> 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
ADD REPLYlink written 7.4 years ago by David Westergaard280
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/arrayQual ityMetrics.html >>>>>>> or at least >>>>>>> >>>>>>> http://www.bioconductor.org/packages/release/bioc/html/arrayQu alityMetrics.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/sel f_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 >>> >>> >>> _______________________________________________ >>> 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
ADD REPLYlink written 7.4 years ago by Daniel Aaen Hansen90
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 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/arrayQua lityMetrics.html >>>>>>>> or at least >>>>>>>> >>>>>>>> http://www.bioconductor.org/packages/release/bioc/html/arrayQ ualityMetrics.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 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 >>>> >>>> >>>> _______________________________________________ >>>> 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 > -- Best wishes Wolfgang Wolfgang Huber EMBL http://www.embl.de/research/units/genome_biology/huber
ADD REPLYlink written 7.4 years ago by Wolfgang Huber13k
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]]
ADD REPLYlink written 7.4 years ago by Daniel Aaen Hansen90
Dear Wolfgang, I have successfully updated cairo graphics library to version 1.10.2. Everything is working, but I am still getting the warnings that Daniel describe. They are of no concern, since it is working, but if you need more info to reproduce the warnings, let me know. Best, David 2012/3/8 Daniel Aaen Hansen <daniel at="" intomics.com="">: > 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 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/arrayQualityMet rics.html > > or at least > > > http://www.bioconductor.org/packages/release/bioc/html/arrayQualityM etrics.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_proce ssed/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 > > > > _______________________________________________ > > 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 > > > > > -- > Best wishes > Wolfgang > > Wolfgang Huber > EMBL > http://www.embl.de/research/units/genome_biology/huber > > >
ADD REPLYlink written 7.4 years ago by David Westergaard280
Dear David the warning from UseMethod("xmlAttrs", node) is bad. It indicates that some or all of the SVG postprocessing needed for the plot interactivity fails. This is likely caused by using an incompatible (i.e. old) version of cairo. I don't think that production of the PNGs has anything to do with what looks to you like a requirement for an X11 connection. It is caused by the function lattice::draw.key, which calls trellis.par.get("fontsize") and to do so, needs an open graphics device. Perhaps what you have seen is that, if no device is open when the above function is encountered within arrayQualityMetrics, your R tries to open an X device, and if that is not available, fails. To circumvent that, you could do something like: pdf("dummy.pdf") source("arrayQualityMetrics.R") dev.off() Re outlier detection threshold, this is explained in the manual page for the function 'outliers': "...boxplotOutliers uses a criterion similar to that used in boxplot.stats to detect outliers in a set of real numbers. The main difference is that in boxplotOutliers, only the outliers to the right (i.e. extraordinarily large values) are detected." At some point, it becomes easier to explain such a thing through code than verbally. The code for boxplotOutliers is: > boxplotOutliers function (x, coef = 1.5) { stats = stats::fivenum(x, na.rm = TRUE) iqr = diff(stats[c(2, 4)]) th = (stats[4] + coef * iqr) list(threshold = th, which = which(x > th)) } <environment: namespace:arrayqualitymetrics=""> Hope this helps. Best wishes wolfganfg David Westergaard scripsit 03/07/2012 10:37 AM: > 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/arrayQual ityMetrics.html >>>>>>> or at least >>>>>>> >>>>>>> http://www.bioconductor.org/packages/release/bioc/html/arrayQu alityMetrics.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/se lf_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 >>> >>> >>> _______________________________________________ >>> 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 -- Best wishes Wolfgang Wolfgang Huber EMBL http://www.embl.de/research/units/genome_biology/huber
ADD REPLYlink written 7.4 years ago by Wolfgang Huber13k
Dear David and Wolfgang, I had the same problem as David with the PNG plots. I could not run arrayQualityMetrics on a remote server while I was offline (eg. through screen). Doing pdf("dummy.pdf") as suggested (or png("dummy.png")), did not help. The solution for me was to set: > options(bitmapType = "cairo") What I found was that the png() function was trying to open an X11 device. According to the png help page, this depends on the graphics device type which is set as a parameter to png(): For ‘type = "Xlib"’ they may not be usable unless the X11 display is available to the owner of the R process. The type can be set manually as a parameter to png(), but the default is set by ‘getOption("bitmapType")’ which defaults to ‘"quartz"’ or ‘"cairo"’ where available, otherwise ‘"Xlib"’. Hence, getOption("bitmapType") ought to be set to 'cairo' on my system since cairo is available, but it was set to 'Xlib': > getOption("bitmapType") [1] "Xlib" Hence, setting: > options(bitmapType = "cairo") solved the problem for me. I don't know why this option is not correctly set on my system. According to our sysadmin, R should be compiled with support for cairo. Some of the options in options() have factory defaults, others are set from environment variables or are platform-dependent. Does anybody know how the option 'bitmapType' is set? Best regards, Daniel On Mar 7, 2012, at 3:04 PM, Wolfgang Huber wrote: > Dear David > > the warning from UseMethod("xmlAttrs", node) is bad. It indicates that some or all of the SVG postprocessing needed for the plot interactivity fails. This is likely caused by using an incompatible (i.e. old) version of cairo. > > I don't think that production of the PNGs has anything to do with what looks to you like a requirement for an X11 connection. It is caused by the function lattice::draw.key, which calls trellis.par.get("fontsize") and to do so, needs an open graphics device. Perhaps what you have seen is that, if no device is open when the above function is encountered within arrayQualityMetrics, your R tries to open an X device, and if that is not available, fails. To circumvent that, you could do something like: > > pdf("dummy.pdf") > source("arrayQualityMetrics.R") > dev.off() > > Re outlier detection threshold, this is explained in the manual page for the function 'outliers': "...boxplotOutliers uses a criterion similar to that used in boxplot.stats to detect outliers in a set of real numbers. The main difference is that in boxplotOutliers, only the outliers to the right (i.e. extraordinarily large values) are detected." At some point, it becomes easier to explain such a thing through code than verbally. The code for boxplotOutliers is: > > > boxplotOutliers > function (x, coef = 1.5) > { > stats = stats::fivenum(x, na.rm = TRUE) > iqr = diff(stats[c(2, 4)]) > th = (stats[4] + coef * iqr) > list(threshold = th, which = which(x > th)) > } > <environment: namespace:arrayqualitymetrics=""> > > > Hope this helps. > > Best wishes > wolfganfg > > > David Westergaard scripsit 03/07/2012 10:37 AM: >> 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/arrayQua lityMetrics.html >>>>>>>> or at least >>>>>>>> >>>>>>>> http://www.bioconductor.org/packages/release/bioc/html/arrayQ ualityMetrics.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/se lf_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 > > > -- > 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 [[alternative HTML version deleted]]
ADD REPLYlink written 7.3 years ago by Daniel Aaen Hansen90
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