A method of processing a sample in a receptacle (10, 300) having a plurality of interconnected chambers in an instrument comprising: a receptacle-receiving area for receiving the receptacle (10, 300); a detector, wherein said detector is a fluorometer having components positioned to detect a fluorescent light signal from the contents of a detection chamber (C28, C322B) of the receptacle (10, 300) when the receptacle (10, 300) is placed in an operative orientation in the receptacle-receiving area; a movable compression element (1154, 1180) positioned to be adjacent the detection chamber (C28, C322B) and located between the receptacle-receiving area and a lens of the detector; a controller (702,730) programmed to move the compression element (1154, 1180) into engagement with a flexible portion of the detection chamber (C28, C322B), thereby depressing the flexible portion to agitate the contents of the detection chamber (C28, C322B) or to move the contents of the detection chamber (C28, C322B) into an adjacently connected chamber of the receptacle (10, 300), and an actuator constructed and arranged to move the compression element (1154, 1180) relative to the detector, wherein the controller (702,730) is programmed to activate the actuator to move the compression element (1154, 1180) into engagement with the flexible portion of the detection chamber (C28, C322B), the method comprising the steps of: (a) moving the compression element (1154, 1180) positioned between the receptacle (10, 300) and the lens of a detector into engagement with a flexible portion of the detection chamber (C28, C322B), thereby depressing the flexible portion to agitate the contents of the detection chamber (C28, C322B) or to move the contents of the detection chamber (C28, C322B) into a directly connected chamber of the receptacle (10, 300); and (b) detecting a light signal from the contents of the detection chamber (C28, C322B) with the detector. a receptacle-receiving area for receiving the receptacle (10, 300); a detector, wherein said detector is a fluorometer having components positioned to detect a fluorescent light signal from the contents of a detection chamber (C28, C322B) of the receptacle (10, 300) when the receptacle (10, 300) is placed in an operative orientation in the receptacle-receiving area; a movable compression element (1154, 1180) positioned to be adjacent the detection chamber (C28, C322B) and located between the receptacle-receiving area and a lens of the detector; a controller (702,730) programmed to move the compression element (1154, 1180) into engagement with a flexible portion of the detection chamber (C28, C322B), thereby depressing the flexible portion to agitate the contents of the detection chamber (C28, C322B) or to move the contents of the detection chamber (C28, C322B) into an adjacently connected chamber of the receptacle (10, 300), and an actuator constructed and arranged to move the compression element (1154, 1180) relative to the detector, wherein the controller (702,730) is programmed to activate the actuator to move the compression element (1154, 1180) into engagement with the flexible portion of the detection chamber (C28, C322B), the method comprising the steps of: (a) moving the compression element (1154, 1180) positioned between the receptacle (10, 300) and the lens of a detector into engagement with a flexible portion of the detection chamber (C28, C322B), thereby depressing the flexible portion to agitate the contents of the detection chamber (C28, C322B) or to move the contents of the detection chamber (C28, C322B) into a directly connected chamber of the receptacle (10, 300); and (b) detecting a light signal from the contents of the detection chamber (C28, C322B) with the detector. (a) moving the compression element (1154, 1180) positioned between the receptacle (10, 300) and the lens of a detector into engagement with a flexible portion of the detection chamber (C28, C322B), thereby depressing the flexible portion to agitate the contents of the detection chamber (C28, C322B) or to move the contents of the detection chamber (C28, C322B) into a directly connected chamber of the receptacle (10, 300); and (b) detecting a light signal from the contents of the detection chamber (C28, C322B) with the detector.