I wish to use the Deseq2 tool on Galaxy but I am unsure how to incorporate the fact that my samples are matched patient samples before and after treatment.
The primary factor that effects gene expression will be Treatment (before and after).
However I also want to account for the secondary factor that each matched sample (before and after) is from a different patient. I don't know how to input this correctly. Do I have to put each patient as a different factor and enter the before and after treatment samples as factor levels?