[BioC] edgeR

Gordon K Smyth smyth at wehi.EDU.AU
Wed Dec 4 05:35:48 CET 2013

Dear Bogdan,

edgeR is updated all the time.  There have been no changes that make the 
package much less sensitive, but the default value for the dispersion 
prior weight was changed some time ago as was the syntax for specifying 
the prior weight.  See help for prior.df in estimateTagwispDisp() and 
estimateGLMTagwiseDisp().  The prior.df determines the amount of squeezing 
that is applied to the tagwise dispersion values.

Best wishes

> Date: Mon, 2 Dec 2013 14:32:24 -0800
> From: Bogdan Tanasa <tanasa at gmail.com>
> To: Steve Lianoglou <lianoglou.steve at gene.com>
> Cc: Janusz Puc <jpuc at ucsd.edu>, F Zhang <fzhang at ucsd.edu>,
> 	Bioconductor mailing list <bioconductor at r-project.org>
> Subject: Re: [BioC] edgeR
> Thanks, Steve ...I was referring to the edgeR version of April 2012.
> On Mon, Dec 2, 2013 at 2:27 PM, Steve Lianoglou <lianoglou.steve at gene.com>wrote:
>> Hi,
>> On Mon, Dec 2, 2013 at 2:20 PM, Bogdan Tanasa <tanasa at gmail.com> wrote:
>>> Dear all,
>>> please could you let me know whether there is any major updates in the
>>> newest version of edgeR
>>> (for Bioconductor version: Release (2.13),
>>> http://www.bioconductor.org/packages/2.13/bioc/html/edgeR.html), as I am
>>> getting a lot less Differentially Expressed Genes than before ...
>> When was "before" (ie. what previous version are you trying to compare to?)
>> Also, this will help:
>> R> news(package="edgeR")
>> -steve
>> --
>> Steve Lianoglou
>> Computational Biologist
>> Genentech

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