Question: Using a countDataSet as input data in DESeq2
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6.0 years ago by
Guest User12k
Guest User12k wrote:
Dear all, This question seems so simple, but I'm struggling to get it right! How to use a countDataSet obtained with easyRNAseq as input data in DESeq2? Thank you very much in advance! Kind regards > countDataSet CountDataSet (storageMode: environment) assayData: 17108 features, 2 samples element names: counts protocolData: none phenoData sampleNames: NS1gallusDNAmapped.bam NS2gallusDNAmapped.bam varLabels: sizeFactor condition varMetadata: labelDescription featureData featureNames: ENSGALG00000000003 ENSGALG00000000004 ... ENSGALG00000029181 (17108 total) fvarLabels: disp_blind fvarMetadata: labelDescription experimentData: use 'experimentData(object)' Annotation: -- output of sessionInfo(): > sessionInfo() R version 3.0.2 (2013-09-25) Platform: x86_64-w64-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] parallel stats graphics grDevices utils datasets methods base other attached packages: [1] DESeq2_1.2.6 RcppArmadillo_0.3.920.3 Rcpp_0.10.6 easyRNASeq_1.8.3 ShortRead_1.20.0 Rsamtools_1.14.2 [7] GenomicRanges_1.14.3 DESeq_1.14.0 lattice_0.20-24 locfit_1.5-9.1 Biostrings_2.30.1 XVector_0.2.0 [13] IRanges_1.20.6 edgeR_3.4.1 limma_3.18.3 biomaRt_2.18.0 Biobase_2.22.0 genomeIntervals_1.18.0 [19] BiocGenerics_0.8.0 intervals_0.14.0 loaded via a namespace (and not attached): [1] annotate_1.40.0 AnnotationDbi_1.24.0 bitops_1.0-6 DBI_0.2-7 genefilter_1.44.0 geneplotter_1.40.0 grid_3.0.2 [8] hwriter_1.3 latticeExtra_0.6-26 LSD_2.5 RColorBrewer_1.0-5 RCurl_1.95-4.1 RSQLite_0.11.4 splines_3.0.2 [15] stats4_3.0.2 survival_2.37-4 XML_3.98-1.1 xtable_1.7-1 zlibbioc_1.8.0 -- Sent via the guest posting facility at bioconductor.org.
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ADD COMMENTlink modified 6.0 years ago by Michael Love26k • written 6.0 years ago by Guest User12k
Answer: Using a countDataSet as input data in DESeq2
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gravatar for Michael Love
6.0 years ago by
Michael Love26k
United States
Michael Love26k wrote:
Hi Natalia, DESeq2 has a different class which can be constructed with the function DESeqDataSetFromMatrix(), which requires a count matrix, a data frame with information about the samples and a design formula. The first two can be extracted from a countDataSet x with counts(x) and pData(x). For more information on the third, check the documentation for DESeq2. I believe that easyRNAseq can also build the DESeqDataSet object directly. Mike On Dec 3, 2013 3:07 AM, "Natalia [guest]" <guest@bioconductor.org> wrote: > > Dear all, > This question seems so simple, but I'm struggling to get it right! How to > use a countDataSet obtained with easyRNAseq as input data in DESeq2? > Thank you very much in advance! > Kind regards > > > countDataSet > CountDataSet (storageMode: environment) > assayData: 17108 features, 2 samples > element names: counts > protocolData: none > phenoData > sampleNames: NS1gallusDNAmapped.bam NS2gallusDNAmapped.bam > varLabels: sizeFactor condition > varMetadata: labelDescription > featureData > featureNames: ENSGALG00000000003 ENSGALG00000000004 ... > ENSGALG00000029181 (17108 total) > fvarLabels: disp_blind > fvarMetadata: labelDescription > experimentData: use 'experimentData(object)' > Annotation: > > > -- output of sessionInfo(): > > > sessionInfo() > R version 3.0.2 (2013-09-25) > Platform: x86_64-w64-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] parallel stats graphics grDevices utils datasets methods > base > > other attached packages: > [1] DESeq2_1.2.6 RcppArmadillo_0.3.920.3 Rcpp_0.10.6 > easyRNASeq_1.8.3 ShortRead_1.20.0 Rsamtools_1.14.2 > [7] GenomicRanges_1.14.3 DESeq_1.14.0 lattice_0.20-24 > locfit_1.5-9.1 Biostrings_2.30.1 XVector_0.2.0 > [13] IRanges_1.20.6 edgeR_3.4.1 limma_3.18.3 > biomaRt_2.18.0 Biobase_2.22.0 genomeIntervals_1.18.0 > [19] BiocGenerics_0.8.0 intervals_0.14.0 > > loaded via a namespace (and not attached): > [1] annotate_1.40.0 AnnotationDbi_1.24.0 bitops_1.0-6 > DBI_0.2-7 genefilter_1.44.0 geneplotter_1.40.0 grid_3.0.2 > [8] hwriter_1.3 latticeExtra_0.6-26 LSD_2.5 > RColorBrewer_1.0-5 RCurl_1.95-4.1 RSQLite_0.11.4 > splines_3.0.2 > [15] stats4_3.0.2 survival_2.37-4 XML_3.98-1.1 > xtable_1.7-1 zlibbioc_1.8.0 > > > -- > Sent via the guest posting facility at bioconductor.org. > [[alternative HTML version deleted]]
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