[BioC] RSEM for transcript and gene level read count and edgeR differential expression analysis

[Steve Lianoglou]

Hi,

On Mon, Aug 19, 2013 at 2:30 PM, Tim Triche, Jr. <tim.triche at gmail.com> wrote:
> http://arxiv.org/pdf/1301.5277v2.pdf may be of interest
>
> voom() transforms everything to log2(RPM) before estimating mean-variance
> trends, so fractional count estimates from RSEM won't impact the modeling
> anyhow.  See also
>
> http://www.statsci.org/smyth/pubs/VoomPreprint.pdf
>
> Personally I've wondered for a long, long time why people spend so much
> time on GLMs for sensitivity, when more biological replicates would make
> more difference.

Money and time.

Time to grow the mouse, I mean ... I wasn't referring to *your* time
as a bioinformatician, no one actually cares about that as long as I
can have the results by tomorrow, thanks! :-)

-steve

-- 
Steve Lianoglou
Computational Biologist
Bioinformatics and Computational Biology
Genentech