Relationship between the Cy5/Cy3 fluorescence ratios measured with antibody microarrays and the concentration ratios of the cognate antigens. The log10 of the Cy5/Cy3 fluorescence ratio was calculated for each antibody spot shown in Figure 1. The median values of the replicate measurements from 12 antibodies were plotted as a function of the concentrations of the corresponding antigens. The error bars represent the standard deviation between the replicate spots. The dashed line represents the known concentration ratio of the cognate antigen. The horizontal dashed line in the Anti-Mint2 panel represents a threshold to assess the reliability of detecting large oncentration changes (see text). It is determined by adding two standard deviations to the value measured at the final dilution.