I want to determine that how far my plants have progressed toward flowering, through the BvFT1 and BvFT2 gene expression. Should I subtract the ΔΔCt of BvFT2 from the ΔΔCt of BvFT1 or I should take another method?
You need to explain more. Are comparing expression level before and after flowering? Do you have a reference gene? Are these genes going opposite directions in term of expression during flowering? Did you measure efficiency of the reaction for both genes?