As I am not exactly an expert in linear modelling and a comprehensive online search did not yield results I'd like to ask for help here:
My experimental design looks as follows: 1 Condition (only individuals with a disease, no controls). Paired treatment design with pre and post treatment, but not the same individuals for both treatments:
My design table thus looks like this:
Patient1 treatment1 baseline Patient1 treatment1 treated Patient2 treatment1 baseline Patient2 treatment1 treated ... Patient3 treatment2 baseline Patient3 treatment2 treated Patient4 treatment2 baseline Patient4 treatment2 treated ...
With a total of 6 patients for one treatment and 7 for the other.
My approach now as to first slice the data and seperate the treatments and look for significantly differently expressed genes seperately withing each treatment (pre vs post treatment). This I just did with the Patient+Timepoint (where Timepoint is the 3rd column, pre/post treatment). However, how would I put the design model if I wanted to look for differentially expressed genes between the two treatments taking into account the pre/post treatment status.
Thank you very much for your help!