arrayQualityMetrics unable to find an inherited method for function \"platformspecific\", for signature \"character\"
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hi, when i running arrayQualityMetrics, i met a broblem like this, Error in function (classes, fdef, mtable): unable to find an inherited method for function "platformspecific", for signature "character". I want to use arrayQualityMetrics to analyse Affymetrix data- after preprocessing. Before using arrayQualityMetrics, i used ReadAffy on my CEL file to get an AffyBatch abject, then used RMA algorithm on the object to obtain a preprocessed dataset, finally called arrayQualityMetrics to analyse the preprocessed, then the error appeared. when called ReadAffy and rma, no erros found, so would u like tell me how to fix that, appreciate very much. And i can call the arrayQualityMetrics on the MLL.A subject provided in the data package ALLMLL without any error. -- output of sessionInfo(): R version 2.14.2 (2012-02-29) Platform: x86_64-pc-mingw32/x64 (64-bit) locale: [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 LC_MONETARY=English_United States.1252 [4] LC_NUMERIC=C LC_TIME=English_United States.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] hgu133acdf_2.9.1 ALLMLL_1.2.11 annotate_1.32.1 affyPLM_1.30.0 [5] preprocessCore_1.16.0 gcrma_2.26.0 affyio_1.22.0 maizecdf_2.9.1 [9] AnnotationDbi_1.16.18 affy_1.32.1 arrayQualityMetrics_3.10.0 Biobase_2.14.0 [13] BiocInstaller_1.2.1 loaded via a namespace (and not attached): [1] beadarray_2.4.1 Biostrings_2.22.0 Cairo_1.5-1 cluster_1.14.2 DBI_0.2-5 [6] genefilter_1.36.0 grid_2.14.2 Hmisc_3.9-2 hwriter_1.3 IRanges_1.12.6 [11] KernSmooth_2.23-7 lattice_0.20-0 latticeExtra_0.6-19 limma_3.10.3 RColorBrewer_1.0-5 [16] RSQLite_0.11.1 setRNG_2009.11-1 splines_2.14.2 survival_2.36-12 SVGAnnotation_0.9-0 [21] tools_2.14.2 vsn_3.22.0 XML_3.9-4.1 xtable_1.7-0 zlibbioc_1.0.1 -- Sent via the guest posting facility at bioconductor.org.
arrayQualityMetrics arrayQualityMetrics • 2.7k views
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Guest User ★ 13k
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Last seen 10.2 years ago
when i running arrayQualityMetrics, i met a broblem like this, Error in function (classes, fdef, mtable): unable to find an inherited method for function "platformspecific", for signature "character". I want to use arrayQualityMetrics to analyse Affymetrix data- after preprocessing. Before using arrayQualityMetrics, i used ReadAffy on my CEL file to get an AffyBatch abject, then used RMA algorithm on the object to obtain a preprocessed dataset, finally called arrayQualityMetrics to analyse the preprocessed, then the error appeared. when called ReadAffy and rma, no erros found, and i can call the arrayQualityMetrics on the MLL.A subject provided in the data package ALLMLL without any error. Following is the commonds i used and the results, GSM162264.CEL is the CEL file got from GEO. >test <- ReadAffy("GSM162264.CEL", widget=getOption("BioC")$affy$use.widgets, celfile.path=NULL, sampleNames=NULL, phenoData=NULL, description=NULL, notes="", rm.mask=FALSE, rm.outliers=FALSE, rm.extra=FALSE, verbose=FALSE,sd=FALSE, cdfname = NULL) >ntest = rma(test) >arrayQualityMetrics(expressionset = "ntest", outdir = "Report_ntest", force = TRUE) The report will be written into directory 'Report_ntest'. Error in function (classes, fdef, mtable) : unable to find an inherited method for function "platformspecific", for signature "character" >test AffyBatch object size of arrays=732x732 features (17 kb) cdf=Maize (17734 affyids) number of samples=1 number of genes=17734 annotation=maize notes= >ntest ExpressionSet (storageMode: lockedEnvironment) assayData: 17734 features, 1 samples element names: exprs protocolData sampleNames: GSM162264.CEL varLabels: ScanDate varMetadata: labelDescription phenoData sampleNames: GSM162264.CEL varLabels: sample varMetadata: labelDescription featureData: none experimentData: use 'experimentData(object)' Annotation: maize so, how should i fix the problem, expecting for your help, appreciate very much. -- output of sessionInfo(): R version 2.14.2 (2012-02-29) Platform: x86_64-pc-mingw32/x64 (64-bit) locale: [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 LC_MONETARY=English_United States.1252 [4] LC_NUMERIC=C LC_TIME=English_United States.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] vsn_3.22.0 limma_3.10.3 hgu133acdf_2.9.1 ALLMLL_1.2.11 [5] annotate_1.32.1 affyPLM_1.30.0 preprocessCore_1.16.0 gcrma_2.26.0 [9] affyio_1.22.0 maizecdf_2.9.1 AnnotationDbi_1.16.18 affy_1.32.1 [13] arrayQualityMetrics_3.10.0 Biobase_2.14.0 BiocInstaller_1.2.1 loaded via a namespace (and not attached): [1] beadarray_2.4.1 Biostrings_2.22.0 Cairo_1.5-1 cluster_1.14.2 DBI_0.2-5 [6] genefilter_1.36.0 grid_2.14.2 Hmisc_3.9-2 hwriter_1.3 IRanges_1.12.6 [11] KernSmooth_2.23-7 lattice_0.20-0 latticeExtra_0.6-19 RColorBrewer_1.0-5 RSQLite_0.11.1 [16] setRNG_2009.11-1 splines_2.14.2 survival_2.36-12 SVGAnnotation_0.9-0 tools_2.14.2 [21] XML_3.9-4.1 xtable_1.7-0 zlibbioc_1.0.1 -- Sent via the guest posting facility at bioconductor.org.
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your call is expected to be arrayQualityMetrics(expressionset = ntest, outdir = "Report_ntest", force = TRUE) note: no quotes around ntest. b On 8 March 2012 12:12, henlen [guest] <guest at="" bioconductor.org=""> wrote: > > when i running arrayQualityMetrics, i met a broblem like this, > Error in function (classes, fdef, mtable): > unable to find an inherited method for function "platformspecific", for signature "character". > I want to use arrayQualityMetrics to analyse Affymetrix data- after preprocessing. > > Before using > arrayQualityMetrics, i used ReadAffy on my CEL file to get an ?AffyBatch abject, > then used RMA algorithm on the object to obtain a preprocessed dataset, > finally called arrayQualityMetrics to analyse the preprocessed, then the error appeared. > > when called ReadAffy and rma, no erros found, > and i can call the arrayQualityMetrics on the MLL.A subject provided in the data package ALLMLL without any error. > > Following is the commonds i used and the results, > GSM162264.CEL is the CEL file got from GEO. > >>test <- ReadAffy("GSM162264.CEL", > ? ? ? ? ? ? ? ? ?widget=getOption("BioC")$affy$use.widgets, > ? ? ? ? ? ? ? ? ?celfile.path=NULL, > ? ? ? ? ? ? ? ? ?sampleNames=NULL, > ? ? ? ? ? ? ? ? ?phenoData=NULL, > ? ? ? ? ? ? ? ? ?description=NULL, > ? ? ? ? ? ? ? ? ?notes="", > ? ? ? ? ? ? ? ? ?rm.mask=FALSE, rm.outliers=FALSE, rm.extra=FALSE, > ? ? ? ? ? ? ? ? ?verbose=FALSE,sd=FALSE, cdfname = NULL) > >>ntest = rma(test) > >>arrayQualityMetrics(expressionset = "ntest", > ? ? ? ? ? ? ? ? ? ? outdir = "Report_ntest", > ? ? ? ? ? ? ? ? ? ? force = TRUE) > The report will be written into directory 'Report_ntest'. > Error in function (classes, fdef, mtable) ?: > ?unable to find an inherited method for function "platformspecific", for signature "character" > > >>test > AffyBatch object > size of arrays=732x732 features (17 kb) > cdf=Maize (17734 affyids) > number of samples=1 > number of genes=17734 > annotation=maize > notes= > >>ntest > ExpressionSet (storageMode: lockedEnvironment) > assayData: 17734 features, 1 samples > ?element names: exprs > protocolData > ?sampleNames: GSM162264.CEL > ?varLabels: ScanDate > ?varMetadata: labelDescription > phenoData > ?sampleNames: GSM162264.CEL > ?varLabels: sample > ?varMetadata: labelDescription > featureData: none > experimentData: use 'experimentData(object)' > Annotation: maize > > so, how should i fix the problem, expecting for your help, appreciate very much. > > ?-- output of sessionInfo(): > > R version 2.14.2 (2012-02-29) > Platform: x86_64-pc-mingw32/x64 (64-bit) > > locale: > [1] LC_COLLATE=English_United States.1252 ?LC_CTYPE=English_United States.1252 ? ?LC_MONETARY=English_United States.1252 > [4] LC_NUMERIC=C ? ? ? ? ? ? ? ? ? ? ? ? ? LC_TIME=English_United States.1252 > > attached base packages: > [1] stats ? ? graphics ?grDevices utils ? ? datasets ?methods ? base > > other attached packages: > ?[1] vsn_3.22.0 ? ? ? ? ? ? ? ? limma_3.10.3 ? ? ? ? ? ? ? hgu133acdf_2.9.1 ? ? ? ? ? ALLMLL_1.2.11 > ?[5] annotate_1.32.1 ? ? ? ? ? ?affyPLM_1.30.0 ? ? ? ? ? ? preprocessCore_1.16.0 ? ? ?gcrma_2.26.0 > ?[9] affyio_1.22.0 ? ? ? ? ? ? ?maizecdf_2.9.1 ? ? ? ? ? ? AnnotationDbi_1.16.18 ? ? ?affy_1.32.1 > [13] arrayQualityMetrics_3.10.0 Biobase_2.14.0 ? ? ? ? ? ? BiocInstaller_1.2.1 > > loaded via a namespace (and not attached): > ?[1] beadarray_2.4.1 ? ? Biostrings_2.22.0 ? Cairo_1.5-1 ? ? ? ? cluster_1.14.2 ? ? ?DBI_0.2-5 > ?[6] genefilter_1.36.0 ? grid_2.14.2 ? ? ? ? Hmisc_3.9-2 ? ? ? ? hwriter_1.3 ? ? ? ? IRanges_1.12.6 > [11] KernSmooth_2.23-7 ? lattice_0.20-0 ? ? ?latticeExtra_0.6-19 RColorBrewer_1.0-5 ?RSQLite_0.11.1 > [16] setRNG_2009.11-1 ? ?splines_2.14.2 ? ? ?survival_2.36-12 ? ?SVGAnnotation_0.9-0 tools_2.14.2 > [21] XML_3.9-4.1 ? ? ? ? xtable_1.7-0 ? ? ? ?zlibbioc_1.0.1 > > -- > Sent via the guest posting facility at bioconductor.org. > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
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