In my lab we have a question about this (we are not experts in bioinformatics by the way, we still learning):
We are doing rna-seq of resistant vs susceptible peppers. I did a DEG analysis using DESEQ2, I got up and down regulated genes using a FDR:0.01 and LFC:0.5. Now I have my respective list of DE genes, but a questions springed to us: with our information is possible to do a "contrast" of genes expression levels using as "control" some house keeping genes ? Like a RT-PCR.