Apparatus and methods for analyzing samples, including for example, samples containing nucleic acids, antibodies, and/or antigens are described. The apparatus may include a frame having a cartridge receiver, two optical devices, thermal cycler, lysis assembly, hybridization heater, and sample transfer assembly. In use, the apparatus may perform multiple sample preparation and analysis processes within the same disposable cartridge including, for example, performing a PCR assay and immunoassay in the same cartridge.