[BioC] which dispersion to choose

Gordon K Smyth smyth at wehi.EDU.AU
Tue Jan 28 23:36:29 CET 2014

Dear Kathrin,

We almost always recommend tagwise moderated dispersions, but it is not a 
choice between trended and tagwise because the moderation is by default 
towards the trend.

Just follow any of the examples in the User's Guide.  Or alternatively use 
the shortcut:

   y <- calcNormFactors(y)
   y <- estimateDisp(y)

which will doing everything for you.

Best wishes

> Date: Mon, 27 Jan 2014 12:23:27 +0100
> From: Ruprecht Kathrin <k.ruprecht at gmx.ch>
> To: <bioconductor at stat.math.ethz.ch>
> Subject: [BioC] which dispersion to choose
> Dear all,
> I'd like to use edgeR to find differently expressed genes in my RNAseq data. My question is which dispersion I should use.
> In a forum I read that moderate tagwise dispersion ranks more highly the DE genes which are consistent in their group - which is what I am looking for.
> How can I achive "moderate" tagwise dispersion or could I use trended dispersion instead?
> My data consists of 18 libraries with 3 treatments (6 libraries each). In these treatments I have 2 groups of 3 libraries each which are not exactly replicates but should behave similarly.
> I want to test mainly for differences between the groups in each treatment.
> Thanks for your Help!
> Kind Regards
> Kathrin Ruprecht
> Master student
> Plant ecological genetics
> ETH Zurich

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