[BioC] DESeq nbinomGLMTest specific comparisons

[Steve Lianoglou]

Hi,

On Tue, Nov 26, 2013 at 8:21 AM, James Floyd <j.a.floyd at qmul.ac.uk> wrote:
> Hi,
>
> I notice in the DESeq vignette<http://bioconductor.org/packages/release/bioc/vignettes/DESeq/inst/doc/DESeq.pdf> there is a "Fixme" comment about including how to test specific comparisons using nbinomGLMTest (page 12). It would be great if someone with experience doing this could let me know how it is done.

Can you be more specific of what you'd like to test? Perhaps you can
setup your problem for us and point out what particular comparison
you'd like to make, and someone can help you better.

Furthermore, if you are using DESeq, you might consider shifting over
to DESeq2. It offers a number of benefits over DESeq, and (I believe)
this is where the DESeq authors are focussing the lion's share of
their attention anyhow.

-steve

-- 
Steve Lianoglou
Computational Biologist
Genentech