A pumping method for use with a pump set to deliver fluid through the pump set to a subject includes determining a duration of time for flushing the first fluid out of the pump set with a second fluid different from the first fluid. A compensated flow rate is calculated for delivering the first fluid through the pump set based on the duration of time for flushing the first fluid out of the pump set. The first fluid is delivered through the pump set at the compensated flow rate.
