Hi everyone, I am currently using DESeq2 in R for performing differential expression analysis on a dataset consisting of 2 conditions (control+treatment) and 4 time points, and there are 3 biological replicates for each condition-timepoint.
So the sample data is as in the attached samp.data image
I would like to find all the genes differentially expressed between time points 1,2 and 3 when compared to time point 0. I want to find all the genes in each condition separately (so all the genes changing in the control and all those changing in the treatment).
What would be the correct design for this? Thanks a lot for your help!