Entering edit mode
This may be a naive question, but I am wondering which, glmFit/glmLRT or glmQLFit/glmQLFTest, I should use for DE gene analysis in paired designs using edgeR. In the edgeR Users Guide (rev 20.4.2016), glmFit/glmLRT is used in Chapter 3.4.1 and 4.1 for paired designs, whereas glmQLFit/glmQLFTest is recommended over glmFit/glmLRT in general in Chapter 2.10.3. I checked a chapter published in Methods Mol Biol (vol 1418, pp391-416, 2016) about Quasi-likelihood methods in edgeR, but there was no mention paired designs in the paper. Is glmFit/glmLRT still preferred for paired designs?
Thank you very much for the clarification as well as the links for the previous posts. Yes, it is easy to swap them. When I compared them yesterday, I found that glmQLFTest is more conservative than glmLRT in general for our RNA-Seq experiments.
My question came up as I found one of the three sets (each in the same paired design) had a lot fewer genes with glmQLFTest (approximately 200 vs 1500). In contrast, at FDR<0.05, the difference is much smaller between glmQLFTest and glmLRT (approximately 1000 vs 2000). The other two sets had much smaller differences between glmQLFTest and glmLRT, probably due to smaller dispersion.
Thanks again for your comments!