With immunoassay or bioassay data, the assay standards often exhibit considerable inter-assay variability. However, the assay controls, which are used to monitor the assay performance and set acceptance criteria, should have no or less interassay variability. In this paper, we develop a mixed-effect calibration model for the assay controls to set new acceptance criteria and qualify the enzyme-linked immunosorbent assay (ELISA) data, which incorporates the interassay variation of assay standards and the nature of the assay controls, and overcomes the problems caused by traditional fixed-effect calibration model.