Dear sir, I am doing differential expression analysis with limma. In ebFit = eBayes(fit2) I am getting error: Error in ebayes(fit = fit, proportion = proportion, stdev.coef.lim = stdev.coef.lim, : No residual degrees of freedom in linear model fits. It is may be because I don't have replicates. So what should I do to for differential expression now. Thank you Nitin Mandloi Sandor Proteomics Pvt. Ltd., hyderabad [[alternative HTML version deleted]]

Without replicates all you can really do is compute fold changes. You might get some traction with the RankProd package, but I have no experience so can't say for sure. Best, Jim On 2/19/2013 8:28 AM, nitin mandloi wrote: > Dear sir, > > I am doing differential expression analysis with limma. In > ebFit = eBayes(fit2) I am getting error: Error in ebayes(fit = fit, > proportion = proportion, stdev.coef.lim = stdev.coef.lim, : No residual > degrees of freedom in linear model fits. It is may be because I don't have > replicates. So what should I do to for differential expression now. > > > > > > Thank you > > Nitin Mandloi > > > > Sandor Proteomics Pvt. Ltd., hyderabad > > > [[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 -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099