Assays for separating magnetic particles include separating magnetically responsive particles from a liquid dispersion disposed in a plurality of reaction vessels, and transporting the reaction vessels in sequence past at least one processing position. A robotics reagent arm and probe dispense reagents into the reaction vessels and a reaction monitoring device is capable of relative movement with respect to the transporting device. Incomplete separation is effected by positioning a magnetic field in contact with the reaction vessel for a first shortened time interval during which the particles partially aggregate and afterwards are removed from the reaction vessel. The magnet is repositioned in contact with the reaction vessel for a third time interval to achieve full separation of particles from the liquid.