create the expression set
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Dear Users, I tried to create the ExpressionSet using the normalized microarray data. >normdata=read.csv("import_transpose_koho.csv", header=T, sep='t', stringsAsFactors =F) ##### read the pheno data >pheno=read.table("sampleInfo.csv", header=T,sep=',',skip=0,stringsAsFactors=F) >pd <- new("AnnotatedDataFrame", data = as.data.frame(pheno)) > Dset<-new("ExpressionSet", exprs=normdata, phenoData=pd) Error in (function (classes, fdef, mtable) : unable to find an inherited method for function ???annotatedDataFrameFrom??? for signature ???"data.frame"??? I am quite new to this, maybe it isn't related to limma package. Does anyone know what's wrong with the dataframe? Thanks a lot for the help, I really appreciate it. -- output of sessionInfo(): > sessionInfo() R version 3.1.0 (2014-04-10) Platform: x86_64-apple-darwin10.8.0 (64-bit) locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] parallel grid stats graphics grDevices utils datasets methods base other attached packages: [1] kohonen_2.0.14 MASS_7.3-33 class_7.3-10 [4] TxDb.Hsapiens.UCSC.hg19.knownGene_2.14.0 gdata_2.13.3 limma_3.20.5 [7] methyAnalysis_1.6.0 methylumi_2.10.0 minfi_1.10.2 [10] bumphunter_1.4.2 locfit_1.5-9.1 iterators_1.0.7 [13] foreach_1.4.2 lattice_0.20-29 matrixStats_0.10.0 [16] ggplot2_1.0.0 reshape2_1.4 scales_0.2.4 [19] FDb.InfiniumMethylation.hg19_2.0.10 BSgenome.Hsapiens.UCSC.hg19_1.3.99 BSgenome_1.32.0 [22] Biostrings_2.32.0 XVector_0.4.0 GenomicFeatures_1.16.2 [25] org.Hs.eg.db_2.14.0 RSQLite_0.11.4 DBI_0.2-7 [28] AnnotationDbi_1.26.0 Biobase_2.24.0 GenomicRanges_1.16.3 [31] GenomeInfoDb_1.0.2 IRanges_1.22.9 BiocGenerics_0.10.0 [34] BiocInstaller_1.14.2 loaded via a namespace (and not attached): [1] affy_1.42.2 affyio_1.32.0 annotate_1.42.0 base64_1.1 BatchJobs_1.2 BBmisc_1.6 [7] beanplot_1.1 BiocParallel_0.6.1 biomaRt_2.20.0 biovizBase_1.12.1 bitops_1.0-6 brew_1.0-6 [13] cluster_1.15.2 codetools_0.2-8 colorspace_1.2-4 dichromat_2.0-0 digest_0.6.4 doRNG_1.6 [19] fail_1.2 Formula_1.1-1 genefilter_1.46.1 GenomicAlignments_1.0.1 genoset_1.16.2 gtable_0.1.2 [25] gtools_3.4.1 Gviz_1.8.3 Hmisc_3.14-4 illuminaio_0.6.0 KernSmooth_2.23-12 latticeExtra_0.6-26 [31] lumi_2.16.0 Matrix_1.1-4 mclust_4.3 mgcv_1.7-29 multtest_2.20.0 munsell_0.4.2 [37] nleqslv_2.2 nlme_3.1-117 nor1mix_1.1-4 pkgmaker_0.22 plyr_1.8.1 preprocessCore_1.26.1 [43] proto_0.3-10 R.methodsS3_1.6.1 RColorBrewer_1.0-5 Rcpp_0.11.2 RCurl_1.95-4.1 registry_0.2 [49] reshape_0.8.5 rngtools_1.2.4 Rsamtools_1.16.1 rtracklayer_1.24.2 sendmailR_1.1-2 siggenes_1.38.0 [55] splines_3.1.0 stats4_3.1.0 stringr_0.6.2 survival_2.37-7 tools_3.1.0 VariantAnnotation_1.10.2 [61] XML_3.98-1.1 xtable_1.7-3 zlibbioc_1.10.0 -- Sent via the guest posting facility at bioconductor.org.
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@james-w-macdonald-5106
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You don't need an ExpressionSet to analyze data using limma. You can instead use a matrix. See ?lmFit for more information. Best, Jim On 6/26/2014 1:59 PM, guest [guest] wrote: > Dear Users, > > I tried to create the ExpressionSet using the normalized microarray data. > >> normdata=read.csv("import_transpose_koho.csv", header=T, sep='t', stringsAsFactors =F) > > ##### read the pheno data >> pheno=read.table("sampleInfo.csv", header=T,sep=',',skip=0,stringsAsFactors=F) >> pd <- new("AnnotatedDataFrame", data = as.data.frame(pheno)) >> Dset<-new("ExpressionSet", exprs=normdata, phenoData=pd) > Error in (function (classes, fdef, mtable) : > unable to find an inherited method for function ???annotatedDataFrameFrom??? for signature ???"data.frame"??? > > I am quite new to this, maybe it isn't related to limma package. Does anyone know what's wrong with the dataframe? > > Thanks a lot for the help, I really appreciate it. > > > > -- output of sessionInfo(): > >> sessionInfo() > R version 3.1.0 (2014-04-10) > Platform: x86_64-apple-darwin10.8.0 (64-bit) > > locale: > [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 > > attached base packages: > [1] parallel grid stats graphics grDevices utils datasets methods base > > other attached packages: > [1] kohonen_2.0.14 MASS_7.3-33 class_7.3-10 > [4] TxDb.Hsapiens.UCSC.hg19.knownGene_2.14.0 gdata_2.13.3 limma_3.20.5 > [7] methyAnalysis_1.6.0 methylumi_2.10.0 minfi_1.10.2 > [10] bumphunter_1.4.2 locfit_1.5-9.1 iterators_1.0.7 > [13] foreach_1.4.2 lattice_0.20-29 matrixStats_0.10.0 > [16] ggplot2_1.0.0 reshape2_1.4 scales_0.2.4 > [19] FDb.InfiniumMethylation.hg19_2.0.10 BSgenome.Hsapiens.UCSC.hg19_1.3.99 BSgenome_1.32.0 > [22] Biostrings_2.32.0 XVector_0.4.0 GenomicFeatures_1.16.2 > [25] org.Hs.eg.db_2.14.0 RSQLite_0.11.4 DBI_0.2-7 > [28] AnnotationDbi_1.26.0 Biobase_2.24.0 GenomicRanges_1.16.3 > [31] GenomeInfoDb_1.0.2 IRanges_1.22.9 BiocGenerics_0.10.0 > [34] BiocInstaller_1.14.2 > > loaded via a namespace (and not attached): > [1] affy_1.42.2 affyio_1.32.0 annotate_1.42.0 base64_1.1 BatchJobs_1.2 BBmisc_1.6 > [7] beanplot_1.1 BiocParallel_0.6.1 biomaRt_2.20.0 biovizBase_1.12.1 bitops_1.0-6 brew_1.0-6 > [13] cluster_1.15.2 codetools_0.2-8 colorspace_1.2-4 dichromat_2.0-0 digest_0.6.4 doRNG_1.6 > [19] fail_1.2 Formula_1.1-1 genefilter_1.46.1 GenomicAlignments_1.0.1 genoset_1.16.2 gtable_0.1.2 > [25] gtools_3.4.1 Gviz_1.8.3 Hmisc_3.14-4 illuminaio_0.6.0 KernSmooth_2.23-12 latticeExtra_0.6-26 > [31] lumi_2.16.0 Matrix_1.1-4 mclust_4.3 mgcv_1.7-29 multtest_2.20.0 munsell_0.4.2 > [37] nleqslv_2.2 nlme_3.1-117 nor1mix_1.1-4 pkgmaker_0.22 plyr_1.8.1 preprocessCore_1.26.1 > [43] proto_0.3-10 R.methodsS3_1.6.1 RColorBrewer_1.0-5 Rcpp_0.11.2 RCurl_1.95-4.1 registry_0.2 > [49] reshape_0.8.5 rngtools_1.2.4 Rsamtools_1.16.1 rtracklayer_1.24.2 sendmailR_1.1-2 siggenes_1.38.0 > [55] splines_3.1.0 stats4_3.1.0 stringr_0.6.2 survival_2.37-7 tools_3.1.0 VariantAnnotation_1.10.2 > [61] XML_3.98-1.1 xtable_1.7-3 zlibbioc_1.10.0 > > -- > 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 > -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099
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Thanks Jim for the reply! I don't proceed to lmFit on limma, I only need to generate ExpressionSet and use it for the SOM. Thanks, Li On 6/26/14 2:51 PM, "James W. MacDonald" <jmacdon at="" uw.edu=""> wrote: >You don't need an ExpressionSet to analyze data using limma. You can >instead use a matrix. See ?lmFit for more information. > >Best, > >Jim > > > >On 6/26/2014 1:59 PM, guest [guest] wrote: >> Dear Users, >> >> I tried to create the ExpressionSet using the normalized microarray >>data. >> >>> normdata=read.csv("import_transpose_koho.csv", header=T, sep='t', >>>stringsAsFactors =F) >> >> ##### read the pheno data >>> pheno=read.table("sampleInfo.csv", >>>header=T,sep=',',skip=0,stringsAsFactors=F) >>> pd <- new("AnnotatedDataFrame", data = as.data.frame(pheno)) >>> Dset<-new("ExpressionSet", exprs=normdata, phenoData=pd) >> Error in (function (classes, fdef, mtable) : >> unable to find an inherited method for function >>???annotatedDataFrameFrom??? for signature ???"data.frame"??? >> >> I am quite new to this, maybe it isn't related to limma package. Does >>anyone know what's wrong with the dataframe? >> >> Thanks a lot for the help, I really appreciate it. >> >> >> >> -- output of sessionInfo(): >> >>> sessionInfo() >> R version 3.1.0 (2014-04-10) >> Platform: x86_64-apple-darwin10.8.0 (64-bit) >> >> locale: >> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 >> >> attached base packages: >> [1] parallel grid stats graphics grDevices utils >>datasets methods base >> >> other attached packages: >> [1] kohonen_2.0.14 MASS_7.3-33 >> class_7.3-10 >> [4] TxDb.Hsapiens.UCSC.hg19.knownGene_2.14.0 gdata_2.13.3 >> limma_3.20.5 >> [7] methyAnalysis_1.6.0 methylumi_2.10.0 >> minfi_1.10.2 >> [10] bumphunter_1.4.2 locfit_1.5-9.1 >> iterators_1.0.7 >> [13] foreach_1.4.2 lattice_0.20-29 >> matrixStats_0.10.0 >> [16] ggplot2_1.0.0 reshape2_1.4 >> scales_0.2.4 >> [19] FDb.InfiniumMethylation.hg19_2.0.10 >>BSgenome.Hsapiens.UCSC.hg19_1.3.99 BSgenome_1.32.0 >> [22] Biostrings_2.32.0 XVector_0.4.0 >> GenomicFeatures_1.16.2 >> [25] org.Hs.eg.db_2.14.0 RSQLite_0.11.4 >> DBI_0.2-7 >> [28] AnnotationDbi_1.26.0 Biobase_2.24.0 >> GenomicRanges_1.16.3 >> [31] GenomeInfoDb_1.0.2 IRanges_1.22.9 >> BiocGenerics_0.10.0 >> [34] BiocInstaller_1.14.2 >> >> loaded via a namespace (and not attached): >> [1] affy_1.42.2 affyio_1.32.0 annotate_1.42.0 >> base64_1.1 BatchJobs_1.2 BBmisc_1.6 >> [7] beanplot_1.1 BiocParallel_0.6.1 biomaRt_2.20.0 >> biovizBase_1.12.1 bitops_1.0-6 brew_1.0-6 >> [13] cluster_1.15.2 codetools_0.2-8 colorspace_1.2-4 >> dichromat_2.0-0 digest_0.6.4 doRNG_1.6 >> [19] fail_1.2 Formula_1.1-1 >>genefilter_1.46.1 GenomicAlignments_1.0.1 genoset_1.16.2 >> gtable_0.1.2 >> [25] gtools_3.4.1 Gviz_1.8.3 Hmisc_3.14-4 >> illuminaio_0.6.0 KernSmooth_2.23-12 >>latticeExtra_0.6-26 >> [31] lumi_2.16.0 Matrix_1.1-4 mclust_4.3 >> mgcv_1.7-29 multtest_2.20.0 munsell_0.4.2 >> [37] nleqslv_2.2 nlme_3.1-117 nor1mix_1.1-4 >> pkgmaker_0.22 plyr_1.8.1 >>preprocessCore_1.26.1 >> [43] proto_0.3-10 R.methodsS3_1.6.1 >>RColorBrewer_1.0-5 Rcpp_0.11.2 RCurl_1.95-4.1 >> registry_0.2 >> [49] reshape_0.8.5 rngtools_1.2.4 Rsamtools_1.16.1 >> rtracklayer_1.24.2 sendmailR_1.1-2 siggenes_1.38.0 >> [55] splines_3.1.0 stats4_3.1.0 stringr_0.6.2 >> survival_2.37-7 tools_3.1.0 >>VariantAnnotation_1.10.2 >> [61] XML_3.98-1.1 xtable_1.7-3 zlibbioc_1.10.0 >> >> -- >> 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 >> > >-- >James W. MacDonald, M.S. >Biostatistician >University of Washington >Environmental and Occupational Health Sciences >4225 Roosevelt Way NE, # 100 >Seattle WA 98105-6099
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On Thu, Jun 26, 2014 at 4:08 PM, Jia, Li (NIH/NCI) [C] <li.jia2@nih.gov> wrote: > Thanks Jim for the reply! > > I don't proceed to lmFit on limma, I only need to generate ExpressionSet > and use it for the SOM. > Hi, Li. You probably do not need an ExpressionSet for SOM, either. However, you can generate a minimal one by doing: Dset = ExpressionSet(assayData=normdata) You can probably add phenoData using: pData(Dset) = pheno Sean > > Thanks, > Li > > On 6/26/14 2:51 PM, "James W. MacDonald" <jmacdon@uw.edu> wrote: > > >You don't need an ExpressionSet to analyze data using limma. You can > >instead use a matrix. See ?lmFit for more information. > > > >Best, > > > >Jim > > > > > > > >On 6/26/2014 1:59 PM, guest [guest] wrote: > >> Dear Users, > >> > >> I tried to create the ExpressionSet using the normalized microarray > >>data. > >> > >>> normdata=read.csv("import_transpose_koho.csv", header=T, sep='t', > >>>stringsAsFactors =F) > >> > >> ##### read the pheno data > >>> pheno=read.table("sampleInfo.csv", > >>>header=T,sep=',',skip=0,stringsAsFactors=F) > >>> pd <- new("AnnotatedDataFrame", data = as.data.frame(pheno)) > >>> Dset<-new("ExpressionSet", exprs=normdata, phenoData=pd) > >> Error in (function (classes, fdef, mtable) : > >> unable to find an inherited method for function > >>‘annotatedDataFrameFrom’ for signature ‘"data.frame"’ > >> > >> I am quite new to this, maybe it isn't related to limma package. Does > >>anyone know what's wrong with the dataframe? > >> > >> Thanks a lot for the help, I really appreciate it. > >> > >> > >> > >> -- output of sessionInfo(): > >> > >>> sessionInfo() > >> R version 3.1.0 (2014-04-10) > >> Platform: x86_64-apple-darwin10.8.0 (64-bit) > >> > >> locale: > >> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 > >> > >> attached base packages: > >> [1] parallel grid stats graphics grDevices utils > >>datasets methods base > >> > >> other attached packages: > >> [1] kohonen_2.0.14 MASS_7.3-33 > >> class_7.3-10 > >> [4] TxDb.Hsapiens.UCSC.hg19.knownGene_2.14.0 gdata_2.13.3 > >> limma_3.20.5 > >> [7] methyAnalysis_1.6.0 methylumi_2.10.0 > >> minfi_1.10.2 > >> [10] bumphunter_1.4.2 locfit_1.5-9.1 > >> iterators_1.0.7 > >> [13] foreach_1.4.2 lattice_0.20-29 > >> matrixStats_0.10.0 > >> [16] ggplot2_1.0.0 reshape2_1.4 > >> scales_0.2.4 > >> [19] FDb.InfiniumMethylation.hg19_2.0.10 > >>BSgenome.Hsapiens.UCSC.hg19_1.3.99 BSgenome_1.32.0 > >> [22] Biostrings_2.32.0 XVector_0.4.0 > >> GenomicFeatures_1.16.2 > >> [25] org.Hs.eg.db_2.14.0 RSQLite_0.11.4 > >> DBI_0.2-7 > >> [28] AnnotationDbi_1.26.0 Biobase_2.24.0 > >> GenomicRanges_1.16.3 > >> [31] GenomeInfoDb_1.0.2 IRanges_1.22.9 > >> BiocGenerics_0.10.0 > >> [34] BiocInstaller_1.14.2 > >> > >> loaded via a namespace (and not attached): > >> [1] affy_1.42.2 affyio_1.32.0 annotate_1.42.0 > >> base64_1.1 BatchJobs_1.2 BBmisc_1.6 > >> [7] beanplot_1.1 BiocParallel_0.6.1 biomaRt_2.20.0 > >> biovizBase_1.12.1 bitops_1.0-6 brew_1.0-6 > >> [13] cluster_1.15.2 codetools_0.2-8 colorspace_1.2-4 > >> dichromat_2.0-0 digest_0.6.4 doRNG_1.6 > >> [19] fail_1.2 Formula_1.1-1 > >>genefilter_1.46.1 GenomicAlignments_1.0.1 genoset_1.16.2 > >> gtable_0.1.2 > >> [25] gtools_3.4.1 Gviz_1.8.3 Hmisc_3.14-4 > >> illuminaio_0.6.0 KernSmooth_2.23-12 > >>latticeExtra_0.6-26 > >> [31] lumi_2.16.0 Matrix_1.1-4 mclust_4.3 > >> mgcv_1.7-29 multtest_2.20.0 munsell_0.4.2 > >> [37] nleqslv_2.2 nlme_3.1-117 nor1mix_1.1-4 > >> pkgmaker_0.22 plyr_1.8.1 > >>preprocessCore_1.26.1 > >> [43] proto_0.3-10 R.methodsS3_1.6.1 > >>RColorBrewer_1.0-5 Rcpp_0.11.2 RCurl_1.95-4.1 > >> registry_0.2 > >> [49] reshape_0.8.5 rngtools_1.2.4 Rsamtools_1.16.1 > >> rtracklayer_1.24.2 sendmailR_1.1-2 siggenes_1.38.0 > >> [55] splines_3.1.0 stats4_3.1.0 stringr_0.6.2 > >> survival_2.37-7 tools_3.1.0 > >>VariantAnnotation_1.10.2 > >> [61] XML_3.98-1.1 xtable_1.7-3 zlibbioc_1.10.0 > >> > >> -- > >> Sent via the guest posting facility at bioconductor.org. > >> > >> _______________________________________________ > >> 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 > >> > > > >-- > >James W. MacDonald, M.S. > >Biostatistician > >University of Washington > >Environmental and Occupational Health Sciences > >4225 Roosevelt Way NE, # 100 > >Seattle WA 98105-6099 > > _______________________________________________ > 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]]
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