[BioC] RNA-Seq, generate batch-free count matrix

[Steve Lianoglou]

Hi Brian,

One comment:

On Sat, Jul 19, 2014 at 8:01 PM, Brian Haas <bhaas at broadinstitute.org> wrote:
[clip]
> In searching the bioconductor mailing list archive, I found:
>
>        edgeR package, removeBatchEffect() function

Beware: this function is part of limma and not edgeR and therefore not
really meant for (raw) count data.

It does handle "voom"ed data, ie. data with weights, but to be
technically/theoretically correct, your downstream analysis must also
be one that deals with observational weights, which I'm guessing is
unlikely.

HTH,
-steve

-- 
Steve Lianoglou
Computational Biologist
Genentech