With agarose beads, it is difficult to thoroughly remove buffer without also disturbing and drawing up some of the pelleted resin. With magnetic beads and a magnet, all the beads are held firmly to the side of the tube, so all buffer can be removed without touching the bead-pellet. Furthermore, agarose typically requires longer incubation times (to enable diffusion of solutions to the internal spaces within) and pre-clearing (to control non-specific bind of unwanted proteins). Because all interactions occur on the outer smooth surface of the magnetic beads, and because they are much more uniform in size, magnetic beads generally provide higher reproducibility and purity compared to agarose. Pre-clearing is usually not necessary with magnetic beads.