An apparatus for performing multi-dimensional assays using a microfluidic chip is presented. The apparatus comprises of two crossing series of micro-channels on the microfluidic chip. The apparatus further comprises of a plurality of magnetic valves placed at the crossings and a guiding magnet. When an operator places the guiding magnet in a vicinity of the chip, the guiding magnet produces a proximal magnetic field gradient at a location of each of the plurality of magnetic valves. At the first micro-channel crossing, a magnetic valve controls fluid flow in the first micro-channel, and another magnetic valve controls fluid flow in the second micro-channel at the first micro-channel crossing. Each magnetic valve comprises a magnetic bead and a cavity on the chip next to a corresponding micro-channel section.