Re: RNA-seq differentially expressed gene finding methods
Richard Friedman <[email protected]> Fri, 5 Sep 2014 12:52:35 -0400
| Newsgroups | gmane.science.biology.informatics.conductor |
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| Message-ID | <[email protected]> |
Dear Son, The t-test assumes a normal distribution, which is appropriate for continous variables. RNAseq data deals with counts (discrete entities). A negative binomial distribution (EdgeR, Deseq) or a mean dependent variance (VOOM) is much more approriate. Also the 3 methods mentioned above estimate variablity better with information from all genes using empirical Bayesian methods, than does the one-gene at-a-time frequentist t-test. 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 Department of Systems Biology Room 824 Irving Cancer Research Center Columbia University 1130 St. Nicholas Ave New York, NY 10032 (212)851-4765 (voice) [email protected] http://friedman.c2b2.columbia.edu/ "There is nothing in my Contemporary Jewish Literature course that is either contemporary, Jewish, or literature". -Rose Friedman, age 17 On Sep 5, 2014, at 12:44 PM, Son Pham wrote: > Dear all, > I know that we have quite very good packages (edgeR, deseq) that calculate > the list of differentially expressed genes in 2 conditions (with > replicates) from raw counts. But I do not know what is wrong with the > following simple approach (and whether other people have been using it): > > 1. Get the (estimated) tpm/fpkm for each gene in each sample > 2. Do a t-test for two groups on each gene. > 3. Adjust the p value for multiple tests (p-adj) > > > Thanks, > > Son. > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > [email protected] > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor _______________________________________________ Bioconductor mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor