create the expression set
1
0
Entering edit mode
Guest User ★ 13k
@guest-user-4897
Last seen 10.3 years ago
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.
limma limma • 1.8k views
ADD COMMENT •
0
Entering edit mode
@james-w-macdonald-5106
Last seen 11 hours ago
United States
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
ADD COMMENT •
0
Entering edit mode
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
ADD REPLY •
0
Entering edit mode
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]]
ADD REPLY •

Login before adding your answer.

Similar Posts
Loading Similar Posts
Traffic: 552 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6