Hi,

I read almost all the posts on time series data analysis using DESEQ2. However, I still have some questions/confusions:

I have a time series data of one same at 4-time points. I need to detect the temporal changes in gene expression profiles over the monitored time course. From what I understand, I accounted for the timepoints in the design formula (for the whole dataset) and then done pairwise comparisons (T2_vs_T1, T3_vsT2 and T4_vs_T3). This will give me LFC changes in the genes expression from one-time point to the other.

I also did he LRT test with the reduced model ~1 and then did pairwise comparisons again. My question is how different this would be from what I did earlier. To determine the early responsive and the late responsive genes which approach would be better.