[BioC] voom transformed data

Gokmen [guest] guest at bioconductor.org
Sat Apr 12 16:35:49 CEST 2014

Dear all,

I am transforming my RNA-Seq count data using voom function of limma package. I need to get the transformed data using the log normalized data (voom.object$E) and the weight matrix (voom.object$weights). I am interested in applying multivariate analysis such as classification and clustering analysis, instead of differential expression. Thus, I want to ask if there is a way to get this transformed data, to work with this data outside limma package.



 -- output of sessionInfo(): 

R version 3.0.3 (2014-03-06)
Platform: x86_64-apple-darwin10.8.0 (64-bit)

[1] C

attached base packages:
[1] parallel  stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] edgeR_3.2.4              tweeDEseqCountData_1.0.9 BiocInstaller_1.10.4    
[4] ReadqPCR_1.6.0           affy_1.38.1              limma_3.16.8            
[7] Biobase_2.20.1           BiocGenerics_0.6.0      

loaded via a namespace (and not attached):
[1] affyio_1.28.0         preprocessCore_1.22.0 tools_3.0.3          
[4] zlibbioc_1.6.0

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