I have cells from 5 healthy patients and 5 disease patients. Cells from each patient were treated with control and treatment conditions.
I would like to do differential expression analysis via DeSeq2 to understand how healthy vs. disease state affects the differential expression of genes between the control and treatment conditions. Within this, I need to control for the patient being the same between each control and treatment condition pair.
I have successfully figured out how to use Deseq2 for a simple analysis (eg just looking at how disease/healthy affect differential expression in the treatment group ONLY as ~Disease), but how would I specify the analysis described above?