Hi, 
Thanks for the info. As in the email I just replied to Dr. Smyth, where I show the data file I used, the raw counts I used are indeed based on genes not transcripts and we are looking for differential gene expression. Are we on the same page?
 
Thanks for the info any way!
best
Ming
 
> From: dstr7320@uni.sydney.edu.au
> To: yi02@hotmail.com
> CC: bioconductor@r-project.org
> Subject: RE: [BioC] questions on edgeR package
> Date: Wed, 29 Jan 2014 02:00:09 +0000
> 
> Hello,
> 
> I made the same mistake last week. I got the same common dispersion estimate for my dataset as you did for your dataset.
> 
> > allExpectedCounts$common.dispersion
> [1] 3.999943
> 
> EdgeR is for differential gene expression, not for differential transcript expression.
> 
> --------------------------------------
> Dario Strbenac
> PhD Student
> University of Sydney
> Camperdown NSW 2050
> Australia
 		 	   		  
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