A reticle is loaded into a lithographic apparatus. The apparatus performs measurements on the reticle, so as to calculate alignment parameters for transferring the pattern accurately to substrates. Tests are performed to detect possible contamination of the reticle or its support. Either operation proceeds with a warning, or the patterning of substrates is stopped. The test uses may use parameters of the alignment model itself, or different parameters. The integrity parameters may be compared against reference values reflecting historic measurements, so that sudden changes in a parameter are indicative of contamination. Integrity parameters may be calculated from residuals of the alignment model. In an example, height residuals are used to calculate parameters of residual wedge (Rx′) and residual roll (Ryy′). From these, integrity parameters expressed as height deviations are calculated and compared against thresholds.