A controller is provided having a circuit that uses non-repeatable run-out data and temperature data to provide a compensation for a fly height of a head. A disk drive may also be provided having a head for reading data from a disk, a thermistor, and a controller for controlling a fly height of the head based on temperature data obtained from the thermistor to refine a pressure determination. A method can include estimating a first pressure by the use of non-repeatable run-out data and temperature data corresponding to a disk drive.