A method for calibrating a pump assembly is disclosed. The method includes characterizing a pump of the pump assembly to determine a performance characteristics of the pump. The method may also include calibrating a sensor associated with a displacement unit of the pump assembly. Calibrating the sensor may include calibrating the sensor under operating conditions of a first environment and under operating conditions of a second environment. Under the operating conditions of the second environment, the pump can also be calibrated to determine a performance characteristics of the pump at the operating conditions of the second environment. The calibrated pump assembly is then used to draw fluid from a subterranean formation or conduct a formation test.