[BioC] DESeq: help with analysis

[Steve Lianoglou]

Hi,

On Tue, Oct 15, 2013 at 10:50 AM, Abhishek Pratap
<abhishek.vit at gmail.com> wrote:
> Hi Everyone
>
> Given the study design( see below) I am somewhat surprised NOT to see any
> genes being differentially expressed with p.adj < .05 or .10. I would like
> the help from folks on this mailing list to introspect the analysis and
> figure out if we overlooked something or data

Providing the code you used for this (not just the plots) would be
helpful, but barring that I'd suggest:

(1) Redo your analysis using DESeq2. It uses a less conservative
over-dispersion estimate per gene, therefore providing more power to
detect differential expression.

(2) Explore your data to see if your replicates cluster together, etc.
Take some guidance from the "Data quality assessment by sample
clustering and visualization" of the DESeq2 vignette.

Optional: you may want to do this analysis with the (looming)
bioc-2.13 version of the packages, but if that's too much of a burden,
use the current release.

HTH,
-steve

-- 
Steve Lianoglou
Computational Biologist
Bioinformatics and Computational Biology
Genentech