Thank you Steve, I appreciate the tip on looking at the prior params and
the email thread.
Best,
Fernando

On Fri, Aug 2, 2013 at 9:25 AM, Steve Lianoglou <lianoglou.steve@gene.com>wrote:

> Hi,
>
> On Fri, Aug 2, 2013 at 7:32 AM, Fernando Biase <fernandobiase@gmail.com>
> wrote:
> > Dear all,
> > I did a RNA-seq analysis two years ago (2011), using edgeR package (I do
> > not remember the version). I was asked to analyze the data again, and
> now I
> > am using edgeR_3.2.4.
> >
> > The comparison is between two groups. The "backbone" of the code was very
> > similar (it is pasted bellow), and I just changed it to adapt the package
> > modifications. It turned out that the number of differentially expressed
> > genes (FDR<0.05) in the second analysis (78) was a smaller than the
> number
> > of DEG obtained in the first analysis (119).
> >
> > I understand that two years is a lot of time in such fast evolving field,
> > and I suppose that the newer package version has more reliable analysis
> > than older version. Nonetheless, has anyone experienced something
> similar?
> > Is there a clear reason for this (other than I am making a mistake)?
>
> This topic comes up every now and again, and I believe it is usually
> due to some changes to the defaults for the prior.df (or prior.n)
> params somewhere.
>
> I'm sure that searching the archives (in the footer of each bioc mail
> is the link to search the archives via gmane) will help to shed more
> light on this, and perhaps this email thread would be a good place to
> start:
>
> http://thread.gmane.org/gmane.science.biology.informatics.conductor/46826
>
> HTH,
> -steve
>
> --
> Steve Lianoglou
> Computational Biologist
> Bioinformatics and Computational Biology
> Genentech
>

	[[alternative HTML version deleted]]

