[BioC] Using a countDataSet as input data in DESeq2

Natalia [guest] guest at bioconductor.org
Tue Dec 3 09:07:53 CET 2013

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
  sampleNames: NS1gallusDNAmapped.bam NS2gallusDNAmapped.bam
  varLabels: sizeFactor condition
  varMetadata: labelDescription
  featureNames: ENSGALG00000000003 ENSGALG00000000004 ... ENSGALG00000029181 (17108 total)
  fvarLabels: disp_blind
  fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'

 -- output of sessionInfo(): 

> sessionInfo()
R version 3.0.2 (2013-09-25)
Platform: x86_64-w64-mingw32/x64 (64-bit)

[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  

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