A computer-controlled method for detecting two or more different fluorescent emission signals emitted from each of a plurality of reaction tubes, each of the plurality of reaction tubes containing a sample, and each of the two or more different fluorescent emission signals being associated with a different nucleic acid which may be present in the sample of at least one of the plurality of reaction tubes, said method comprising, for each reaction tube and each fluorescent emission signal to be detected, the steps of: (a) incubating the contents of the reaction tubes within a real-time rotary incubator that includes, for each fluorescent emission signal to be detected, an optical detection module configured to perform real-time fluorescence detection of a reaction tube positioned within the real-time rotary incubator at a signal-detecting position with respect to that optical detection module to determine the amount of a target nucleic acid within the sample contained within the reaction tube, wherein the signal detecting position for each optical detection moduli is at a different location within the real-time rotary incubator, wherein the real-time rotary incubator further includes a rotating multiple tube unit carousel assembly, wherein said carousel is motor-driven and constructed and arranged for holding, moving, and positioning the reaction tubes with respect to said optical detection modules, and wherein said carousel is configured to carry a plurality of radially oriented, circumferentially-arranged reaction tubes within the real-time rotary incubator, the reaction tubes being arranged in multiple tube units, the multiple tube units being integrally formed linear arrays of reaction tubes; (b) moving the reaction tube to the signal-detecting position with respect to that optical detection module with said carousel configured to sequentially place the reaction tubes carried on the multiple tube units into the signal-detecting position for each optical detection module; (c) directing, by the optical detection module, an optical excitation signal at the reaction tube, the optical excitation signal having a known wavelength that excites an associated fluorescent emission signal having a known emission wavelength, wherein the optical excitation signal has a known excitation frequency; (d) detecting an optical signal with the optical detection module, wherein the optical signal includes any fluorescent emission signal emitted by the contents of the reaction tube at the signal-detecting position; and (e) with a phase detector circuit, discarding any portion of the detected optical signal having a frequency that is inconsistent with the known excitation frequency to determine the portion of the detected optical signal that corresponds to the associated fluorescent emission signal. (a) incubating the contents of the reaction tubes within a real-time rotary incubator that includes, for each fluorescent emission signal to be detected, an optical detection module configured to perform real-time fluorescence detection of a reaction tube positioned within the real-time rotary incubator at a signal-detecting position with respect to that optical detection module to determine the amount of a target nucleic acid within the sample contained within the reaction tube, wherein the signal detecting position for each optical detection moduli is at a different location within the real-time rotary incubator, wherein the real-time rotary incubator further includes a rotating multiple tube unit carousel assembly, wherein said carousel is motor-driven and constructed and arranged for holding, moving, and positioning the reaction tubes with respect to said optical detection modules, and wherein said carousel is configured to carry a plurality of radially oriented, circumferentially-arranged reaction tubes within the real-time rotary incubator, the reaction tubes being arranged in multiple tube units, the multiple tube units being integrally formed linear arrays of reaction tubes; (b) moving the reaction tube to the signal-detecting position with respect to that optical detection module with said carousel configured to sequentially place the reaction tubes carried on the multiple tube units into the signal-detecting position for each optical detection module; (c) directing, by the optical detection module, an optical excitation signal at the reaction tube, the optical excitation signal having a known wavelength that excites an associated fluorescent emission signal having a known emission wavelength, wherein the optical excitation signal has a known excitation frequency; (d) detecting an optical signal with the optical detection module, wherein the optical signal includes any fluorescent emission signal emitted by the contents of the reaction tube at the signal-detecting position; and (e) with a phase detector circuit, discarding any portion of the detected optical signal having a frequency that is inconsistent with the known excitation frequency to determine the portion of the detected optical signal that corresponds to the associated fluorescent emission signal.