I am beginning a project that will require me run upwards of 1000 individual full qPCR plates to measure the natural variation in gene copy number (mito genes). I have access to two departmental thermocyclers, a newer model and a older model. I would like to run all of my samples on the newest thermocycler however its availability is limited. I was suggested to use both thermocycler to collect my data, but I am concerned if using two different models would inject some variability into my data. I am especially concerned since the nature of the project is to measure the natural variability of the samples. Are my concerns warranted? Would reviewers for publication have an issue with this?