Hallo everyone

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!

There is an example in the vignette for just this design, see the section about “group specific condition effects...”