A reference microplate is described herein which can be used to help calibrate and troubleshoot an optical interrogation system. In one embodiment, the reference microplate has a frame with an array of wells each of which contains an optical biosensor and each optical biosensor is at least partially coated with a substance (e.g., elastomer, optical epoxy). In another embodiment, the reference microplate in addition to having its optical biosensors at least partially covered with a substance (e.g., elastomer, optical epoxy) also has a controllable heating device attached thereto which is used to heat the optical biosensors.