Methods and apparatus for generating a variable clock used to control a component of a substrate processing system are provided herein. In some embodiments, an apparatus for controlling a substrate processing system includes: a phase locked loop circuit for generating a relative clock that is phase locked to a variable frequency signal being used by a substrate processing chamber; and a controller, coupled to the phase locked loop circuit, for producing a control signal for a component of the substrate processing system, wherein the control signal is based upon the relative clock and an operating indicia of the substrate processing system.