A laboratory automation system that is capable of carrying out clinical chemistry assays, immunoassays, amplification of nucleic acid assays, and any combination of the foregoing, said laboratory automation system employing at least one of micro-well plates and deep multi-well plates as reaction vessels. The use of micro-well plates as reaction vessels enables the laboratory automation system to assume a variety of arrangements, i.e., the laboratory automation system can comprise a variety of functional modules that can be arranged in various ways. In order to effectively carry out immunoassays by means of micro-well plates, a technique known as inverse magnetic particle processing can be used to transfer the product(s) of immunoassays from one micro-well of a micro-well plate to another.