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.) -Ryan 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 >> >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >