The new version of DESeq is more conservative — we've seen this too. As far
as I understand, this is because of a change in the way it shares
information between per-gene empirical variance estimates and the fitted
variance (which is parametric and no longer local in the new version).
There is some good information on the bottom of page 6 of the vignette:
http://www.bioconductor.org/packages/release/bioc/vignettes/DESeq/inst/doc/DESeq.pdf

HTH,
Vince

On Mon, Mar 12, 2012 at 3:50 PM, Abhishek Pratap <apratap@lbl.gov> wrote:

> Hi Todd
>
> I have seen this behaviour when I reduce the number of replicates to
> 0. I am assuming in your case with both the DESeq versions you are
> using same number of replicates. Also in case you are not using
> replicates at all then I believe it can affect the latest .DESeq
> model. I am not sure about the version 1.2.
>
> -Abhi
>
> On Mon, Mar 12, 2012 at 3:11 PM, Creasy, Todd <tcreasy@som.umaryland.edu>
> wrote:
> > Hi,
> >
> > We're comparing an older version of DESeq with the new 1.6 version and
> I'm finding a large discrepancy.  Probably an option I'm missing or
> something.  In the samples I'm working with, I see total DE genes going
> from ~200 - 2000 genes at FDR = 0.10 to nearly 0 genes using the new
> version at the same FDR.
> >
> > What could be going on here.  Admittedly, the old version was 1.2 so we
> were way behind but I'm still shocked by this drop off.
> >
> > Thoughts?
> >
> > todd
> >
> >        [[alternative HTML version deleted]]
> >
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-- 
Vince Buffalo
Statistical Programmer
Bioinformatics Core
UC Davis Genome Center
vincebuffalo.com twitter.com/vsbuffalo

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