Go for the best reproducibility. In our hands, this means the Lightcycler. In any case: the first thing you should always do is: check your reproducibility in multiple samples distributed over several tubes/capillaries. We do not experience any difference between plastic and glass capillaries. Plastic is more durable and less expensive. In our hands Roche performs superior to any other mix we have tried. Unfortunately, it is also the most expensive. As a cheaper alternative we have found that Takara’s is almost as good. The combination of TaKaRa mix, plastic capillaries and reduced reaction volume allows us to cut the running cost in half. Simplify your calculations by running a standard curve in the place of the delta Ct method. If your reproducibility is satisfactory, you can run single determinations. At that point you can spend your duplicates on repeating the biological experiment, in the place of repeating the real time amplification. We wish you good luck.