Methods for thermally calibrating reaction chambers are provided. In some embodiments, methods may include calculating a first correction factor of a first contact type temperature sensor within a first reaction chamber utilizing a first temperature sensor and applying the first correction factor to a first temperature controller to provide a first calibrated contact type temperature sensor. Embodiments may also include calculating a first calibration factor of a first non-contact type temperature sensor within the first reaction chamber utilizing the first calibrated contact type temperature sensor and applying the first calibration factor to the first non-contact type temperature sensor to provide a first calibrated non-contact type temperature sensor.