The system is a clinical multiplex instrument intended to measure and sort multiple signals generated my multiple probes, intercalating dyes, or other ligands in an assay from a clinical sample. Signals may be generated by fluorescence or other phenomena and may be measured using filters on a photodiode or other detector. It may integrate sample and/or reagent handling, amplification, dedicated instrument control, data acquisition software, raw data storage mechanisms and other essential hardware components along with the signal reader unit. The system is used with specific assays to comprise an assay test system.