Dear Rich,

 From what I can tell, it should be possible. The development version of 
DESeq2 implements the DSS "squeezing" method combined with edgeR's 
Cox-Reid dispersion estimation. You could use DESeq2 to estimate 
dispersions, and then copy those dispersion values into an edgeR DGEList 
object. Then you can use edgeR::glmQLFTest, which implements 
(approximately) the QuasiSeq method.

I have not had time yet to investigate putting these packages together 
in this way, but it is something I plan to look at. I'm certain that the 
combination is technically possible, and I'm reasonably sure that the 
result would be statistically meaningful.

-Ryan Thompson

On Mar 12, 2013 7:06 AM, "Richard Friedman" 
<friedman@cancercenter.columbia.edu 
<mailto:friedman@cancercenter.columbia.edu>> wrote:

    Dear List.

             The papers on DSS (included in Bioconductor):

    Wu H, Wang C, Wu Z. A new shrinkage estimator for dispersion improves
    differential expression detection in RNA-seq data. Biostatistics. 2013
    Apr;14(2):232-43.

    and  QuasiSeq (included in CRAN):

      Lund SP, Nettleton D, McCarthy DJ, Smyth GK. Detecting
    differential expression
    in RNA-sequence data using quasi-likelihood with shrunken dispersion
    estimates.
    Stat Appl Genet Mol Biol. 2012

    both give evidence of superior performance to edgeR (if I understand
    them correctly).

    Have the two methods been compared?
    Can the 2 methods been combined (with DSS estimating the dispersion
    used in
    the quasi-negative bionomial disribution used in QuasiSeq)?

    I would appreciate any insight with respect to what is the overall best
    method for differential expression in RNASeq available at present.

    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)/
    Columbia Initiative in Systems Biology
    Room 824
    Irving Cancer Research Center
    Columbia University
    1130 St. Nicholas Ave
    New York, NY 10032
    (212)851-4765 (voice)
    friedman@cancercenter.columbia.edu
    <mailto:friedman@cancercenter.columbia.edu>
    http://cancercenter.columbia.edu/~friedman/
    <http://cancercenter.columbia.edu/%7Efriedman/>

    Fritz Lang. Didn't he do "Star Trek".
    -Rose Friedman, age 16


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