A lithographic apparatus is a machine that applies a desired pattern onto a substrate, usually onto a target portion of the substrate. A functional relationship between local height deviations across a substrate and focus information, such as a determined focus amount, is determined for a substrate, e.g., a reference substrate. Height deviations are subsequently measured for another substrate, e.g. a production substrate. The height deviations for the subsequent substrate and the functional relationship are used to determine predicted focus information for the subsequent substrate. The predicted focus information is then used to control the lithographic apparatus to apply a product pattern to the product substrate.