In a computer-controlled, automated method, a nucleic acid amplification procedure is performed within a prescribed incubation temperature range within an instrument that comprises at least one thermal element situated at a first location of the instrument and an amplification incubator situated at a second, spaced-apart location of the instrument. A receptacle and its contents are exposed to the thermal element for a predetermined period of time at the first location, such that the temperature of the contents of the receptacle is adjusted to approximate the incubation temperature. The receptacle is then moved from the first location and into the amplification incubator, and, in the amplification incubator, a nucleic acid contained in the contents of the receptacle is subjected to the nucleic acid amplification procedure.