As far as I'm aware, the same strategy described for doing limma time course analysis with splines would also apply to GLM-based methods for RNA-seq like edgeR, On Wed 13 Mar 2013 10:55:13 AM PDT, Steve Lianoglou wrote: > Hi Sandra, > > On Wed, Mar 13, 2013 at 12:22 PM, Sandra Rehan <sandra.rehan at="" gmail.com=""> wrote: >> I am looking for software to analyze time course data for an Illumina >> gene expression data set (four lanes of paired end reads). I have two >> biological replicates for seven time points. All packages that I am >> aware of (bats, time course, edge) are designed for microarray data >> analysis. Does someone know of a software package designed for >> Illumina time course data? > > There has been a recent thread on this list about doing a "proper" > timecourse analysis w/ limma using splines -- this thread resulted in > Gordon adding an additional section to the limma user's guide on how > to do so. > > I wonder if you couldn't just use limma::voom to hammer your data into > a limma-workable-object and just do the timecourse analysis as > suggested w/ the microarray data? > > HTH, > -steve >