I've run a series of multiplex PCR experiments on a StepOne Plus instrument using ABI TaqMan assays with GAPDH as my endogenous control. Due to the number of samples I have run each target over 5 plates. I purchased a Human RNA control from Life Technologies and included this on each plate. I had intended to use this as both my reference sample and as an interplate calibrator. However, I've run some cytokines off e.g. IL-6 and they aren't expressed in this RNA control but the GAPDH does show expression. I'm performing ddCT analysis and so I intend to use another of my own samples as the reference sample now instead and analyse the data manually. What is the best way to account for interplate variability in this situation?