A method and system are provided that reduce the effect of substantially non-random electrical interference on an input device's ability to reliably and accurately sense the position of an object. Several embodiments improve performance of an input device by reducing the effect of interference on position sensing data acquired by the input device. In one embodiment, the input device corrects for a cyclic variation in the electromagnetic interference (EMI) generated by components within the electronic system, such as interference from refreshing or updating an image on a display module that affects the capacitive sensing measurements acquired from a plurality of capacitive sensing elements. However, in some embodiments, performance of an input device is improved by reducing the effect that external interference generated outside of the electronic system has on the position sensing data acquired by the input device.