[BioC] voom transformed data

[Gordon K Smyth]

Dear Gokmen,

You ask how to get the data from voom, but you clearly already know how to 
get voom.object$E and voom.object$weights, which is the output from voom.

Are you hoping that there is some way to combine these two quantities, so 
that the weights are no longer needed?  No there isn't.  The whole point 
of the voom method is to keep the log-cpm values and weights separate. 
As the published paper explains, the output should be used with software 
that is able to make use of the precision weights.

If you want to obtain log-cpm or log-rpkm values for clustering, then I 
suggest the cpm() or rpkm() functions in the edgeR package.

Best wishes
Gordon


> Date: Sat, 12 Apr 2014 07:35:49 -0700 (PDT)
> From: "Gokmen [guest]" <guest at bioconductor.org>
> To: bioconductor at r-project.org, gokmenzararsiz at hotmail.com
> Subject: [BioC] voom transformed data
>
>
> 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.
>
> Thanks,
>
> Gokmen
>
> -- output of sessionInfo():
>
> R version 3.0.3 (2014-03-06)
> Platform: x86_64-apple-darwin10.8.0 (64-bit)
>
> locale:
> [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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