
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@cancercenter.columbia.edu
http://cancercenter.columbia.edu/~friedman/

In memoriam, Ray Bradbury






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