INTRODUCTION: Typically, bead-based assays ("bead arrays") use the mean or median value of a population of measurements to judge ligand binding or other activity, which results in a change in fluorescence intensity. Individual bead measurements are used here to calculate population parameters integral to the measurement of a bead array. METHODS: Using a commercially-available instrument designed for bead array measurements, a set of beads were labeled with biotin and then titrated with PE-Streptavidin. Data were collected under normal machine conditions as well as variations. RESULTS: The "sensitivity" of the measurements was determined using parametric and nonparametric statistical methods as well as regression analysis over a limited range of the titration (concentration vs. response profile). CONCLUSIONS: Results at low ligand concentrations suggest that precise measurements with bead array systems require a large number of individual bead measurements to be acquired. Individual bead measurements should be used to determine the mean and confidence intervals for the calculated measurements. These results also apply to regression analysis of concentration-response profiles. Furthermore, features of the instrument can be manipulated to achieve increased sensitivity and detection of lower amounts of ligand bound to the bead populations. Copyright (c) 2006 International Society for Analytical Cytology.