[BioC] DeSeq vs current version of Cuffdiff

[Richard Friedman]

Dear Bioconductor list,

	Sometime ago Simon Anders explained the difference
between DeSeq and Cuffdiff as follows:

"If you have two samples, cuffdiff tests, for each transcript, whether
there is evidence that the concentration of this transcript is not the
same in the two samples.

If you have two different experimental conditions, with replicates for
each condition, DESeq tests, whether, for a given gene, the change in
expression strength between the two conditions is large as compared to
the variation within each replicate group."

Current language on the Cuffdiff site suggests that the current version
of that program  tests for whether the change is significant compared to
changes in each condition.

http://cufflinks.cbcb.umd.edu/howitworks.html#hdif

http://cufflinks.cbcb.umd.edu/howitworks.html#reps

Can someone please comment on the relative merits of Cuffdiff and
DeSeq. I ask here because our sequencing core delivers results
based on Cuffdiff and I want to know if I should redo it using
DeSeq,I would greatly appreciate any guidance in this matter.

Thanks and best wishes,
Rich
------------------------------------------------------------
Richard A. Friedman, PhD
Associate Research Scientist,
Biomedical Informatics Shared Resource
Herbert Irving Comprehensive Cancer Center (HICCC)
Lecturer,
Department of Biomedical Informatics (DBMI)
Educational Coordinator,
Center for Computational Biology and Bioinformatics (C2B2)/
National Center for Multiscale Analysis of Genomic Networks (MAGNet)
Room 824
Irving Cancer Research Center
Columbia University
1130 St. Nicholas Ave
New York, NY 10032
(212)851-4765 (voice)
friedman at cancercenter.columbia.edu
http://cancercenter.columbia.edu/~friedman/

I am a Bayesian. When I see a multiple-choice question on a test and I  
don't
know the answer I say "eeney-meaney-miney-moe".

Rose Friedman, Age 14