Methods and apparatus for in-situ calibration of a flow controller are provided herein. In some embodiments, a method of flowing a gas includes providing a flow controller configured to provide a first gas at a first value of a flow rate based on a calculated first relationship determined by using a standard gas; determining an actual first relationship between the flow rate and the setpoint for the first gas from a plurality of values of the flow rate of the first gas determined at a corresponding plurality of values of the setpoint of the flow controller, wherein each of the plurality of values of the flow rate is determined from flowing the first gas through the flow controller at corresponding ones of the plurality of values for the setpoint; and flowing the first gas at the first value of the flow rate based on the actual first relationship.