We have recently conducted an experiment but I am not sure if I am using the right way to analyze it. Please give me some inputs about this.

We want to look at the differentially expressed genes in wildtype and mutant mouse, and we collected the primary cells and put them in 3 different culture conditions.(Lets say these are control condition, condition A and condition B) Can I divide (FPKM mutant condition A/FPKM mutant control condition) by (FPKM wildtype condition A/ FPKM wildtype control condition) and say the value I got is the Fold change at condition A? From that, I further look at the genes that have 2 fold higher or 0.5 fold lower and define them as the significantly changed genes by the mutation in condition A.

Does this sound reasonable to you guys?