Hi, I have two experiments in the first I have cells of type A treated and cells of type A not treated.
In the second I have cells of type B wild type and cell of type C wild type.
I would like to perform these comparisons: A treated VS A not treated and B wild type VS C wild type and compare the FC between the two analyses of some genes.
What is the best method to do this using DESeq2?
Should I perform two separate analyses with DESeq2 and then compare the FC?
Or should I load the four conditions in the same object and to use the contrast in order to do the comparisons?