[BioC] QuasiSeq vs DSS

Ryan C. Thompson rct at thompsonclan.org
Tue Mar 12 20:15:25 CET 2013

Here is a quote from Gordon Smyth a few months ago in response to a 
question of mine, which I think neatly summarizes the relationship 
between QuasiSeq and edgeR::glmQLFTest:

> glmQLFTest() and QuasiSeq were developed independently with the same 
> idea, hence we got together to write the paper. If you use common 
> dispersion to fit the linear model, then glmQLFTest() is like 
> NegBinQLShrink. If you use trended dispersion to fit the linear model 
> (recommended), then glmQLFTest() is like NegBinQLSpline. They are not 
> quite identical however. glmQLTest() leverages the functionality of 
> the edgeR and limma packages, whereas QuasiSeq has used its own 
> implementations of everything. The latter are described in the paper.
(Gordon, I hope you don't mind me posting this publically. Hopefully it 
saves you the trouble of rewriting it.)


On Tue 12 Mar 2013 10:11:25 AM PDT, Richard Friedman wrote:
> Dear Ryan,
> Thank you for your response.
> 3 questions:
> 1. If I had just a simple pairwise comparison is it known DSS or 
> QuasiSeq better?
> 2. I was unaware that an approximate implementation of QuasiSeq was 
> available in
> edgeR. If so, is it known hor it compare to the ordinairy EdgeR on the 
> one hand and the
> full QuasiSeq on the other.
> 3. And I guess that the third question is for Gordon - Is using DSS 
> and QuasiSeq (or EdgeR) together
> desireable and if so, are there plans to incorporate DSS into QuasiSeq 
> (EdgeR).
> My note was planning ahead. I will still be in the microarray world 
> for a more few weeks
> before I return to learning RNASeq. I wanted to know what the best 
> practice is.
> If you (or anybody out there) develops a script to meld the two 
> methods, I am sure that
> it would be interesting to the list.
> Best wishes,
> Rich
> On Mar 12, 2013, at 12:59 PM, Ryan C. Thompson wrote:
>> 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 at 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 at cancercenter.columbia.edu
>> http://cancercenter.columbia.edu/~friedman/
>> Fritz Lang. Didn't he do "Star Trek".
>> -Rose Friedman, age 16
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