A substrate has a plurality of overlay gratings formed thereon by a lithographic process. Each overlay grating has a known overlay bias. The values of overlay bias include for example two values in a region centered on zero and two values in a region centered on P/2, where P is the pitch of the gratings. Overlay is calculated from asymmetry measurements for the gratings using knowledge of the different overlay bias values, each of the overall asymmetry measurements being weighted by a corresponding weight factor. Each one of the weight factors represents a measure of feature asymmetry within the respective overlay grating. The calculation is used to improve subsequent performance of the measurement process, and/or the lithographic process. Some of the asymmetry measurements may additionally be weighted by a second weight factor in order to eliminate or reduce the contribution of phase asymmetry to the overlay.