Greetings, I have a sample with four different conditions: 1uE, 10 uE, 100uE, 500uE The conditions are analyzed as pairs: 1uE vs10 uE 1uE vs 100 uE 1uE vs 500uE Using the examples in the DESeq tutorial it appears that I would have to analyze these pairs as having no replicates but I'm thinking I really have four replicates. Is there a way to calculate the dispersion using all of the data and then extract the pairs for DE analysis? Thanks, Bill [[alternative HTML version deleted]]

Hi, On Mon, Feb 13, 2012 at 7:30 PM, Willie Nelson <nelson.wd at="" gmail.com=""> wrote: > Greetings, > I have a sample with four different conditions: > > 1uE, 10 uE, 100uE, 500uE > > The conditions are analyzed as pairs: > 1uE vs10 uE > 1uE vs 100 uE > 1uE vs 500uE > > Using the examples in the DESeq tutorial it appears that I would have to > analyze these pairs as having no replicates but I'm thinking I really have > four replicates. Oh? So you're trying to identify genes differentially expressed between replicates? :-) -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology ?| Memorial Sloan-Kettering Cancer Center ?| Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact