Hi folks, I'm currently attempting some time-course analysis of a recent RNA-Seq run using WGCNA. I have 5 time points, with 4 biological replicates of 2 conditions at each point, so around 40 samples total. The main problem that I'm having is simply one of confusion. I'm not sure exactly how to include the time-course information and sample-matching to WGCNA. Reading through the tutorials, time-course data is simply not added to the experimental design frame.

Perhaps my problem is coming from not understanding exactly how the analysis progresses.

Any help would be greatly appreciated.