I have 30 paired-end samples with 6 replicates in 5 groups (4 treatments + 1 baseline control). I am trying to decide how to setup the DE analysis. The glm approach would be the best design, but I'm not clear how to setup the design and comparisons with the baseline sample. Would I use the baseline group as an intercept and compare all treatments to baseline? How would I also include comparisons between each treatment that also takes into account the baseline?