i think you can use as you mentioned that you are using single segments.. so you mean a single Gene? then also there you run internal control as Actin and GAPDH in each plate or just in One plate and use that plate again and again?.. If you are sure that there is less variation in all the plates then can go on with Gene study option,,,most researcher suggests standard curve method for analysis but is not must to follow that.. but is considered better one.