Substrate processing including correction for deposition location is described, including a combinatorial processing chamber that incorporates the correction. The combinatorial processing chamber can be used to process multiple regions of a substrate using different processing parameters on different regions. For example, one region can have one material deposited on it and another region can have a different material deposited on it, although other combinations and variations are possible. The combinatorial processing chamber uses a rotating and revolving substrate pedestal to be able to deposit on all locations or positions on a substrate. The combinatorial processing chamber uses a correction factor that accounts for variations in alignment and/or configuration of the processing chamber so that the actual location of deposition of a region is approximately the same as a desired location of deposition.