Question: arrayQualityMetrics and NChannelSets
0
gravatar for Tim Rayner
8.2 years ago by
Tim Rayner270
Tim Rayner270 wrote:
Hi, Just a quick note to observe that the current stable version of arrayQualityMetrics seems to have a problem with NChannelSet objects: > nc NChannelSet (storageMode: lockedEnvironment) assayData: 1178100 features, 50 samples element names: exprs protocolData rowNames: GWAS16.10_160_CD16.CEL GWAS16.11_158_CD16.CEL ... GWAS16.L_148_CD16.CEL (50 total) varLabels: exprs dates varMetadata: labelDescription channel phenoData rowNames: GWAS16.10_160_CD16.CEL GWAS16.11_158_CD16.CEL ... GWAS16.L_148_CD16.CEL (50 total) varLabels: info.batch.name operator ... visual_check (62 total) varMetadata: labelDescription channel featureData: none experimentData: use 'experimentData(object)' Annotation: pd.hugene.1.1.st.v1 > arrayQualityMetrics(nc) The directory 'arrayQualityMetrics report for nc' has been created. Error in rep("#1F78B4", x$numArrays) : invalid 'times' argument > traceback() 4: intgroupColors(x) 3: append(x, intgroupColors(x)) 2: prepdata(expressionset, intgroup = intgroup, do.logtransform = do.logtransform) 1: arrayQualityMetrics(nc) > validObject(nc) [1] TRUE > sessionInfo() R version 2.13.1 (2011-07-08) Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) locale: [1] en_GB.UTF-8/en_GB.UTF-8/C/C/en_GB.UTF-8/en_GB.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] arrayQualityMetrics_3.8.0 pd.hugene.1.1.st.v1_3.2.0 [3] oligo_1.16.0 preprocessCore_1.14.0 [5] oligoClasses_1.14.0 RSQLite_0.9-4 [7] DBI_0.2-5 ClinStudyWeb_0.2.4 [9] rjson_0.2.5 SmithLabArray_0.5.5 [11] limma_3.8.3 Biobase_2.12.2 loaded via a namespace (and not attached): [1] affxparser_1.24.0 affy_1.30.0 affyio_1.20.0 [4] affyPLM_1.28.5 annotate_1.30.1 AnnotationDbi_1.14.1 [7] beadarray_2.2.0 Biostrings_2.20.3 bit_1.1-7 [10] Cairo_1.4-9 cluster_1.14.0 ff_2.2-3 [13] gdata_2.8.1 genefilter_1.34.0 gplots_2.10.1 [16] grid_2.13.1 gtools_2.6.2 Hmisc_3.8-3 [19] hopach_2.12.0 hwriter_1.3 IRanges_1.10.6 [22] lattice_0.19-33 latticeExtra_0.6-18 RColorBrewer_1.0-5 [25] RCurl_1.6-10 setRNG_2009.11-1 splines_2.13.1 [28] survival_2.36-9 SVGAnnotation_0.9-0 tcltk_2.13.1 [31] tools_2.13.1 vsn_3.20.0 XML_3.4-3 [34] xtable_1.5-6 Given that the documentation claims to support such objects I'm assuming this is a bug? I'm currently coercing GeneFeatureSet objects to NChannelSet and as you can see the conversion yields valid objects. As a workaround, is there an alternative class to which I should be coercing? Many thanks, Tim Rayner -- Bioinformatician Smith Lab, CIMR University of Cambridge
• 762 views
ADD COMMENTlink modified 8.1 years ago by Wolfgang Huber13k • written 8.2 years ago by Tim Rayner270
Answer: arrayQualityMetrics and NChannelSets
0
gravatar for Wolfgang Huber
8.2 years ago by
EMBL European Molecular Biology Laboratory
Wolfgang Huber13k wrote:
Dear Tim thank you for your feedback and sorry for the delayed reply. arrayQualityMetrics has changed a lot recently, and there may be some hickups. Can you please try with a more recent (devel) version of arrayQualityMetrics, and if the problem persists, send me the offending object 'nc'? As a quick workaround, can you try with converting to 'ExpressionSet' instead of 'NChannelSet'? I have just tried library(CCl4) library(arrayQualityMetrics) data(CCl4) arrayQualityMetrics(CCl4) which worked without error,and also this quality report http://www-huber.embl.de/users/whuber/bioc- list/110916/Report_for_nCCl4_with_RIN was made by code in the package vignette from the NChannelSet nCCl4. Best wishes Wolfgang > sessionInfo() R Under development (unstable) (2011-09-25 r57072) Platform: x86_64-apple-darwin10.8.0/x86_64 (64-bit) locale: [1] C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] arrayQualityMetrics_3.9.4 CCl4_1.0.9 [3] limma_3.9.18 Biobase_2.13.9 [5] fortunes_1.4-2 loaded via a namespace (and not attached): [1] AnnotationDbi_1.15.21 BiocInstaller_1.1.28 Biostrings_2.21.9 [4] Cairo_1.4-9 DBI_0.2-5 Hmisc_3.8-3 [7] IRanges_1.11.27 KernSmooth_2.23-6 RColorBrewer_1.0-5 [10] RSQLite_0.9-4 SVGAnnotation_0.9-0 XML_3.4-3 [13] affy_1.31.5 affyPLM_1.29.3 affyio_1.21.2 [16] annotate_1.31.1 beadarray_2.3.8 cluster_1.14.0 [19] genefilter_1.35.0 grid_2.14.0 hwriter_1.3 [22] lattice_0.19-33 latticeExtra_0.6-18 preprocessCore_1.15.0 [25] reshape_0.8.4 setRNG_2009.11-1 splines_2.14.0 [28] survival_2.36-9 tools_2.14.0 vsn_3.21.2 [31] xtable_1.5-6 zlibbioc_0.1.7 Sep/22/11 12:29 PM, Tim Rayner scripsit:: > Hi, > > Just a quick note to observe that the current stable version of > arrayQualityMetrics seems to have a problem with NChannelSet objects: > >> nc > NChannelSet (storageMode: lockedEnvironment) > assayData: 1178100 features, 50 samples > element names: exprs > protocolData > rowNames: GWAS16.10_160_CD16.CEL GWAS16.11_158_CD16.CEL ... > GWAS16.L_148_CD16.CEL (50 total) > varLabels: exprs dates > varMetadata: labelDescription channel > phenoData > rowNames: GWAS16.10_160_CD16.CEL GWAS16.11_158_CD16.CEL ... > GWAS16.L_148_CD16.CEL (50 total) > varLabels: info.batch.name operator ... visual_check (62 total) > varMetadata: labelDescription channel > featureData: none > experimentData: use 'experimentData(object)' > Annotation: pd.hugene.1.1.st.v1 > > >> arrayQualityMetrics(nc) > The directory 'arrayQualityMetrics report for nc' has been created. > Error in rep("#1F78B4", x$numArrays) : invalid 'times' argument > > >> traceback() > 4: intgroupColors(x) > 3: append(x, intgroupColors(x)) > 2: prepdata(expressionset, intgroup = intgroup, do.logtransform = > do.logtransform) > 1: arrayQualityMetrics(nc) > > >> validObject(nc) > [1] TRUE > > >> sessionInfo() > R version 2.13.1 (2011-07-08) > Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) > > locale: > [1] en_GB.UTF-8/en_GB.UTF-8/C/C/en_GB.UTF-8/en_GB.UTF-8 > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] arrayQualityMetrics_3.8.0 pd.hugene.1.1.st.v1_3.2.0 > [3] oligo_1.16.0 preprocessCore_1.14.0 > [5] oligoClasses_1.14.0 RSQLite_0.9-4 > [7] DBI_0.2-5 ClinStudyWeb_0.2.4 > [9] rjson_0.2.5 SmithLabArray_0.5.5 > [11] limma_3.8.3 Biobase_2.12.2 > > loaded via a namespace (and not attached): > [1] affxparser_1.24.0 affy_1.30.0 affyio_1.20.0 > [4] affyPLM_1.28.5 annotate_1.30.1 AnnotationDbi_1.14.1 > [7] beadarray_2.2.0 Biostrings_2.20.3 bit_1.1-7 > [10] Cairo_1.4-9 cluster_1.14.0 ff_2.2-3 > [13] gdata_2.8.1 genefilter_1.34.0 gplots_2.10.1 > [16] grid_2.13.1 gtools_2.6.2 Hmisc_3.8-3 > [19] hopach_2.12.0 hwriter_1.3 IRanges_1.10.6 > [22] lattice_0.19-33 latticeExtra_0.6-18 RColorBrewer_1.0-5 > [25] RCurl_1.6-10 setRNG_2009.11-1 splines_2.13.1 > [28] survival_2.36-9 SVGAnnotation_0.9-0 tcltk_2.13.1 > [31] tools_2.13.1 vsn_3.20.0 XML_3.4-3 > [34] xtable_1.5-6 > > Given that the documentation claims to support such objects I'm > assuming this is a bug? I'm currently coercing GeneFeatureSet objects > to NChannelSet and as you can see the conversion yields valid objects. > As a workaround, is there an alternative class to which I should be > coercing? > > Many thanks, > > Tim Rayner > -- Wolfgang Huber EMBL http://www.embl.de/research/units/genome_biology/huber
ADD COMMENTlink written 8.2 years ago by Wolfgang Huber13k
Answer: arrayQualityMetrics and NChannelSets
0
gravatar for Wolfgang Huber
8.1 years ago by
EMBL European Molecular Biology Laboratory
Wolfgang Huber13k wrote:
Dear Tim thank you. You were right: previous versions of the 'arrayQualityMetrics' function expected elements 'R' and 'G' in the 'assayData' slot of the 'NChannelSet', and otherwise failed with the cryptic error message that you reported. I have now added some logic to the 'arrayQualityMetrics' function so that if it sees an 'exprs' element in 'assayData' (what you have in 'nc') it simply invokes the same behaviour as for 'ExpressionSet'. I also added better error reporting if neither of these two cases apply, and documented this behaviour in the vignette. See arrayQualityMetrics >= 3.9.5, and also here: http://www-huber.embl.de/users/whuber/bioc-list/110929/Report_for_nc which was produced by library("arrayQualityMetrics") load("nc.RData") arrayQualityMetrics(nc, do.logtransform=TRUE) To respond to your below questions, I think the behaviour of the validity method of NChannelSet class does the right thing. The problem lied on the side of 'arrayQualityMetrics' function, who assumed more specific properties of these objects (namely, the number and name of its assayData elements). Thanks again for this useful feedback, it helps a lot to make this package run on a wide variety of datasets. Hope this helps Wolfgang Sep/27/11 11:54 AM, Tim Rayner scripsit:: > Dear Wolfgang, > > Thank you very much for your reply. I've tried using the latest devel > version of arrayQualityMetrics and I'm afraid the error persists > (sessionInfo is below). The offending nc object is in my public > dropbox, here: http://dl.dropbox.com/u/1225281/nc.RData > > I've also tried coercing the NChannelSet object to an ExpressionSet, > but that also fails: > >> as(nc, 'ExpressionSet') > Error in updateOldESet(from, "ExpressionSet") : > no slot of name "pData" for this object of class "AnnotatedDataFrame" > > I've tried loading the convert library (v 1.28.0) but that doesn't > make any difference. Converting from the original GeneFeatureSet > object also fails with the same message. I can load the CCl4 object > and confirm that arrayQualityMetrics runs without problems on that > object. > > Having looked through the code I've come to the conclusion that the > problem is likely to be me attempting to use the wrong data class; I > guess NChannelSet is designed solely for use with two-channel data, so > "N" in this scenario shouldn't equal 1. The assayData slot for nc > contains a slot named 'exprs', rather than the 'R', 'G', 'Rb', 'Gb', > etc. slots which are expected. Why the validObject() function fails to > flag this is probably a topic for a separate discussion. > > Given that I presumably shouldn't be using NChannelSet, and the > coercion from GeneFeatureSet to ExpressionSet currently doesn't work, > I'm wondering if there's any way to run arrayQualityMetrics on > unnormalised data sets prepared using the oligo package? > > Many thanks again, > > Tim > > >> sessionInfo() > R version 2.13.0 (2011-04-13) > Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) > > locale: > [1] C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] arrayQualityMetrics_3.9.4 pd.hugene.1.0.st.v1_3.2.0 > [3] oligo_1.16.2 preprocessCore_1.14.0 > [5] oligoClasses_1.14.0 RSQLite_0.9-4 > [7] DBI_0.2-5 SmithLabArray_0.5.5 > [9] limma_3.8.3 Biobase_2.12.2 > > loaded via a namespace (and not attached): > [1] AnnotationDbi_1.14.1 Biostrings_2.20.3 Cairo_1.4-9 > [4] Hmisc_3.8-3 IRanges_1.10.6 RColorBrewer_1.0-5 > [7] SVGAnnotation_0.9-0 XML_3.4-3 affxparser_1.24.0 > [10] affy_1.30.0 affyPLM_1.28.5 affyio_1.20.0 > [13] annotate_1.30.1 beadarray_2.2.0 bit_1.1-7 > [16] cluster_1.14.0 ff_2.2-3 gdata_2.8.1 > [19] genefilter_1.34.0 gplots_2.10.1 grid_2.13.0 > [22] gtools_2.6.2 hopach_2.12.0 hwriter_1.3 > [25] lattice_0.19-33 latticeExtra_0.6-18 setRNG_2009.11-1 > [28] splines_2.13.0 survival_2.36-9 vsn_3.20.0 > [31] xtable_1.5-6 > > > > On 26 September 2011 09:30, Wolfgang Huber<whuber at="" embl.de=""> wrote: >> Dear Tim >> >> thank you for your feedback and sorry for the delayed reply. >> arrayQualityMetrics has changed a lot recently, and there may be some >> hickups. >> >> Can you please try with a more recent (devel) version of >> arrayQualityMetrics, and if the problem persists, send me the offending >> object 'nc'? >> >> As a quick workaround, can you try with converting to 'ExpressionSet' >> instead of 'NChannelSet'? >> >> I have just tried >> >> library(CCl4) >> library(arrayQualityMetrics) >> data(CCl4) >> arrayQualityMetrics(CCl4) >> >> which worked without error,and also this quality report >> http://www-huber.embl.de/users/whuber/bioc- list/110916/Report_for_nCCl4_with_RIN >> was made by code in the package vignette from the NChannelSet nCCl4. >> >> Best wishes >> Wolfgang >> >> >>> sessionInfo() >> R Under development (unstable) (2011-09-25 r57072) >> Platform: x86_64-apple-darwin10.8.0/x86_64 (64-bit) >> >> locale: >> [1] C >> >> attached base packages: >> [1] stats graphics grDevices utils datasets methods base >> >> other attached packages: >> [1] arrayQualityMetrics_3.9.4 CCl4_1.0.9 >> [3] limma_3.9.18 Biobase_2.13.9 >> [5] fortunes_1.4-2 >> >> loaded via a namespace (and not attached): >> [1] AnnotationDbi_1.15.21 BiocInstaller_1.1.28 Biostrings_2.21.9 >> [4] Cairo_1.4-9 DBI_0.2-5 Hmisc_3.8-3 >> [7] IRanges_1.11.27 KernSmooth_2.23-6 RColorBrewer_1.0-5 >> [10] RSQLite_0.9-4 SVGAnnotation_0.9-0 XML_3.4-3 >> [13] affy_1.31.5 affyPLM_1.29.3 affyio_1.21.2 >> [16] annotate_1.31.1 beadarray_2.3.8 cluster_1.14.0 >> [19] genefilter_1.35.0 grid_2.14.0 hwriter_1.3 >> [22] lattice_0.19-33 latticeExtra_0.6-18 preprocessCore_1.15.0 >> [25] reshape_0.8.4 setRNG_2009.11-1 splines_2.14.0 >> [28] survival_2.36-9 tools_2.14.0 vsn_3.21.2 >> [31] xtable_1.5-6 zlibbioc_0.1.7 >> >> >> >> Sep/22/11 12:29 PM, Tim Rayner scripsit:: >>> >>> Hi, >>> >>> Just a quick note to observe that the current stable version of >>> arrayQualityMetrics seems to have a problem with NChannelSet objects: >>> >>>> nc >>> >>> NChannelSet (storageMode: lockedEnvironment) >>> assayData: 1178100 features, 50 samples >>> element names: exprs >>> protocolData >>> rowNames: GWAS16.10_160_CD16.CEL GWAS16.11_158_CD16.CEL ... >>> GWAS16.L_148_CD16.CEL (50 total) >>> varLabels: exprs dates >>> varMetadata: labelDescription channel >>> phenoData >>> rowNames: GWAS16.10_160_CD16.CEL GWAS16.11_158_CD16.CEL ... >>> GWAS16.L_148_CD16.CEL (50 total) >>> varLabels: info.batch.name operator ... visual_check (62 total) >>> varMetadata: labelDescription channel >>> featureData: none >>> experimentData: use 'experimentData(object)' >>> Annotation: pd.hugene.1.1.st.v1 >>> >>> >>>> arrayQualityMetrics(nc) >>> >>> The directory 'arrayQualityMetrics report for nc' has been created. >>> Error in rep("#1F78B4", x$numArrays) : invalid 'times' argument >>> >>> >>>> traceback() >>> >>> 4: intgroupColors(x) >>> 3: append(x, intgroupColors(x)) >>> 2: prepdata(expressionset, intgroup = intgroup, do.logtransform = >>> do.logtransform) >>> 1: arrayQualityMetrics(nc) >>> >>> >>>> validObject(nc) >>> >>> [1] TRUE >>> >>> >>>> sessionInfo() >>> >>> R version 2.13.1 (2011-07-08) >>> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) >>> >>> locale: >>> [1] en_GB.UTF-8/en_GB.UTF-8/C/C/en_GB.UTF-8/en_GB.UTF-8 >>> >>> attached base packages: >>> [1] stats graphics grDevices utils datasets methods base >>> >>> other attached packages: >>> [1] arrayQualityMetrics_3.8.0 pd.hugene.1.1.st.v1_3.2.0 >>> [3] oligo_1.16.0 preprocessCore_1.14.0 >>> [5] oligoClasses_1.14.0 RSQLite_0.9-4 >>> [7] DBI_0.2-5 ClinStudyWeb_0.2.4 >>> [9] rjson_0.2.5 SmithLabArray_0.5.5 >>> [11] limma_3.8.3 Biobase_2.12.2 >>> >>> loaded via a namespace (and not attached): >>> [1] affxparser_1.24.0 affy_1.30.0 affyio_1.20.0 >>> [4] affyPLM_1.28.5 annotate_1.30.1 AnnotationDbi_1.14.1 >>> [7] beadarray_2.2.0 Biostrings_2.20.3 bit_1.1-7 >>> [10] Cairo_1.4-9 cluster_1.14.0 ff_2.2-3 >>> [13] gdata_2.8.1 genefilter_1.34.0 gplots_2.10.1 >>> [16] grid_2.13.1 gtools_2.6.2 Hmisc_3.8-3 >>> [19] hopach_2.12.0 hwriter_1.3 IRanges_1.10.6 >>> [22] lattice_0.19-33 latticeExtra_0.6-18 RColorBrewer_1.0-5 >>> [25] RCurl_1.6-10 setRNG_2009.11-1 splines_2.13.1 >>> [28] survival_2.36-9 SVGAnnotation_0.9-0 tcltk_2.13.1 >>> [31] tools_2.13.1 vsn_3.20.0 XML_3.4-3 >>> [34] xtable_1.5-6 >>> >>> Given that the documentation claims to support such objects I'm >>> assuming this is a bug? I'm currently coercing GeneFeatureSet objects >>> to NChannelSet and as you can see the conversion yields valid objects. >>> As a workaround, is there an alternative class to which I should be >>> coercing? >>> >>> Many thanks, >>> >>> Tim Rayner >>> >> >> >> -- >> >> >> 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 >> -- Wolfgang Huber EMBL http://www.embl.de/research/units/genome_biology/huber
ADD COMMENTlink written 8.1 years ago by Wolfgang Huber13k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 291 users visited in the last hour