It is very difficult to compare all thes results. Perhaps best is you may like to decide first what is the purpose of your study and choose the analysis. If you can confirm in the downstream analysis, that should be it. Partek and Cuffdiff uses a totally different approach.
 
Best.
 


--- On Fri, 10/14/11, Lana Schaffer <schaffer@scripps.edu> wrote:


From: Lana Schaffer <schaffer@scripps.edu>
Subject: [BioC] RNA-Seq : comparison cuffdiff, edgeR, Partek
To: "'bioconductor@r-project.org'" <bioconductor@r-project.org>
Date: Friday, October 14, 2011, 1:59 AM


Hi,
I have done RNA-Seq using cuffdiff, edgeR, and Partek software
And get a different list of differential expressed transcripts
For all the software.
Has anyone have any comments about this?

Lana Schaffer
Biostatistics, Informatics
DNA Array Core Facility
858-784-2263


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