I have a question regarding differential expression using DEseq. I have 2 plant tissues (leaf and stem) and 2 species (A and B) with 3 biological replicate each. After performing differential expression using DEseq, can i compare the top 10 differential expressed genes and see how their RPKM values are compared? For example for gene1 can i calculate ratio of RPKM between A/B for leaf and stem respectively?
I wanted to do this so that i have two independent analyses (one using RPKM and the other using DEseq). Am i thinking correct or i need to compare the differential expressed genes with normalized counts or no need to compare at all. Any help is appreciated.