Apparatus and methods are used to calibrate an array of individually controllable elements within a lithographic apparatus. A calibration unit can switch between a first state in which the modulated beam of radiation passes into a projection system for projecting the modulated beam of radiation onto a substrate and a second state in which a portion of the modulated beam of radiation is inspected by the calibration unit. The calibration unit generates calibration data, or alternatively, updates calibration data, based on the inspection of the modulated beam of radiation. An array controller uses the calibration data to provide control signals to elements of an array of individually controllable elements, which are subsequently configured in response to the control signals.