Analysis of each synthetic target hybridized independently to assess cross-hybridization. Panel A. Color map of independent hybridizations. Each column (x-axis) represents a slide to which a single synthetic target was hybridized (1–108). Each row (y-axis) represents a clonotype specific probe (1–108). Self-hybridization is normalized to 1. Panel B. The degree of cross hybridization is plotted against the number of nucleotide differences between probe:synthetic target pairs. Cross-hybridization arises from probe:synthetic target pairs that differ by one base. Panel C. Comparison of the measured normalizer intensity versus their expected profile. A good linear relationship is evident with R = 0.68, p < 0.001.