[BioC] limma-voom

[Gordon K Smyth]

Hi Ming,

voom is part of the limma package.  There is a voom case study in the 
limma User's Guide with complete working code.  It is the last case study 
in the users guide.

voom works fine with either counts, or fractional counts, or scaled 
counts.

We are currently finalizing additional voom code to detect differential 
splicing.  That code isn't in the public package, but will be soon.

Best wishes
Gordon

On Thu, 30 Jan 2014, Ming Yi wrote:

> I found the following documents
>
> http://stuff.mit.edu/afs/athena/software/r/r_v2.15.1/lib/R/library/limma/html/voom.html
> http://www.bioconductor.org/packages/release/bioc/vignettes/limma/inst/doc/usersguide.pdf
> http://www.statsci.org/smyth/pubs/VoomPreprint.pdf
>
> But I could not find the real limma-voom package document. Is voom just 
> as normalization function prior to using limma linear model? Any good 
> examples of case study of working commands available as example?
>
> Thanks again!
> Ming

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