Methods and apparatus treat a respiratory disorder. For example, a pressure generator supplies a flow of air at positive pressure to a patient's airway through a patient interface. A sensor generates a signal representing respiratory flow rate of the patient. A controller controls the pressure generator to provide to the patient interface a ventilation therapy having a base pressure. The controller computes a measure of ventilation of the patient from the signal. The controller computes a measure of flow limitation from an inspiratory portion of the signal. The controller computes a ratio of the measure of ventilation and an expected normal ventilation. The controller adjusts a set point for the base pressure of the ventilation therapy based on the measure of flow limitation. The adjustment may further depend on a comparison between the ratio and a relative ventilation threshold that increases as the measure of flow limitation increases.