Hello,

I have an experimental design as: condition: infection 1 or infection 2 timepoints: 0hr (baseline), 12, 24, 48hrs post-infection

I want to perform several analyses. (1) i want to be able to see DE gene expression time point vs baseline (which i think is just simple 1-parameter deseq2, which is easy to run with the vignette) (2) i want to be able to compare a specific time point in infection 1 vs infection 2 (ie. infection 1, 12hrs vs infection 2, 12hrs). However, as these are different infections, do I need to somehow perform a normalization to baseline (the baseline state for these 2 different infections are different)? How would I do this?

Thanks !

do I need to somehow perform a normalization to baseline

If you want to compare two things, just compare two things. Adding in the variability from a third thing will not help things.

Do like the vignette suggests. Make a new infection_timepoint column of ColData, and that's your design, you use that contrast in your results call.