The supplement mentioned by the authors in their final paragraph is also attached (here). It is worth at least a glance. I wonder whether the notoriously anticonservative Wald test is responsible for recovering information lost to over-shrinkage. On Mon, Nov 26, 2012 at 10:20 AM, Tim Triche, Jr. <tim.triche at="" gmail.com="">wrote: > I think he means > > A new shrinkage estimator for dispersion improves differential expression > detection in RNA-seq data. > http://www.ncbi.nlm.nih.gov/pubmed/23001152 > > which outlines an empirical Bayes method to improve estimation of the > Gamma parameters in the Gamma-Poisson (i.e. negative binomial) formulation > of the count model. Other authors have proposed generalized Poisson, > beta-binomial, Laplace mixture models, etc. for similar purposes, and Dr. > Smyth has presented extensive empirical results for the existing edgeR > formulations via Cox-Reid estimation along a sliding scale from > "individual" to "completely shared" variance (Gamma). > > On the other hand, the authors (Hao Wu and Jean Wu, at least) are Hopkins > alumni, if I'm not mistaken, and the corresponding author wrote the SQN > package, so I can't imagine an implementation of DSS for use in edgeR is > too terribly far off. However: > > We find that most of the improvement obtained in DSS is due to the > different dispersion estimate, as > passing the DSS estimates to edgeR/DESeq yields very similar results as in > DSS (supplementary material > available at Biostatistics online, Figure S9). Both the edgeR and the > DESeq methods have been expanded > to now accommodate multiclass comparisons. Our test is currently limited > to two-class comparison and it > is our immediate plan to extend the dispersion estimators to multifactor > designs. With an estimate of the > dispersion, one can use generalized linear models as done in McCarthy and > others (2012). > > The paper is open-access and thus attached. Perhaps the authors (of any > of the above works) can comment. > > > On Mon, Nov 26, 2012 at 9:38 AM, Richard Friedman < > friedman at cancercenter.columbia.edu> wrote: > >> >> On Nov 26, 2012, at 12:30 PM, aec [guest] wrote: >> >> >> >> > >> > Is it possible to adopt the CQN normalization method (Hansen, 2012) as >> an option of the edgeR function 'calcNormFactors' ? And the new shrinkage >> estimator for dispersion (Wu, 2012) that seems to be better than the >> currently used by edgeR ? >> > >> > thanks, >> > >> > >> >> Dear Aec, >> >> Is it possible you mean this paper: >> >> 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 Oct 22;11(5). doi:pii: >> /j/sagmb.2012.11.issue-5/1544-6115.1826/1544-6115.1826.xml. >> 10.1515/1544-6115.1826. PubMed PMID: 23104842. >> If not, please give the complete reference to the Wu paper. >> 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/ >> >> In memoriam, Ray Bradbury >> >> >> >> >> >> >> > -- output of sessionInfo(): >> > >> > any >> > >> > -- >> > Sent via the guest posting facility at bioconductor.org. >> > >> > _______________________________________________ >> > 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 >> >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> 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 >> > > > > -- > *A model is a lie that helps you see the truth.* > * > * > Howard Skipper<http: cancerres.aacrjournals.org="" content="" 31="" 9="" 1173.full.pdf=""> > > -- *A model is a lie that helps you see the truth.* * * Howard Skipper<http: cancerres.aacrjournals.org="" content="" 31="" 9="" 1173.full.pdf=""> -------------- next part -------------- A non-text attachment was scrubbed... Name: kxs033supp.pdf Type: application/pdf Size: 1973404 bytes Desc: not available URL: <https: stat.ethz.ch="" pipermail="" bioconductor="" attachments="" 20121126="" 35e5b52a="" attachment-0001.pdf="">