A lithographic apparatus comprises an illumination system, an array of individually controllable elements, a substrate table, a projection system, a position encoder, an imaging device, and an image processing unit. The illumination system conditions a radiation beam. The array of individually controllable elements modulates the cross-section of the radiation beam. The substrate table supports a substrate. The projection system projects the modulated radiation beam onto a target portion of the substrate, thereby applying a pattern to the target portion of the substrate. The pattern comprises a first line and a second line. The first line is offset from the second line. The position encoder determines a position of the substrate table. The position encoder comprises a position sensor and a scale. The scale comprises a plurality of lines intended to be straight and parallel to one another. The imaging device obtains an image of the first line and the second line. The image processing unit measures the separation between the first line and the second line in a plurality of locations, and determines the non-uniformity of at least a part of the scale from the plurality of separations.