I have an RNA-seq experiment that is similar to section 3.5 in the edgeR user’s guide, i.e. a nested paired approach, and I have used this approach to analyze my own data. Briefly, the experiment involves 60 RNA samples, corresponding to two groups of bacterial strains (commensal (C) and disease-causing (D)); each group consisting of 15 different strains; either strain treated (IND) and not treated with a chemical (CTR). My questions are about estimating dispersion in this type of scenario (which is skipped in the user’s guide):
- Can I correctly estimate common/trended and tagvise dispersion using estimateGLMCommonDisp /estimateGLMTrendedDisp and estimateGLMTagwiseDisp (relative to a design matrix), even though there are no true biological replicates?
- How do I calculate the prior degrees of freedom in this case?
Any help will be greatly appreciated.