real time PCR machine choice - (May/18/2006 )

We're planning to use a published protocol for diagnostic testing using real time PCR. Should it matter much if we used a different brand of PCR machine as the one in the protocol? Can you just optimize, for example, a LightCycler kit with a Rotor-Gene machine?

From my experiences, LightCycler abd Rotor-Gene don't have much different in term of machine performanace. Both are manufacture by same company, Idaho Technology.