Factors affecting the boundary bias and implications for signal ratios in competitive hybridizations.

<p>(A) Hybridization of labeled RNA (single-color) at a range of concentrations (75–4,500 ng) for 18 h. (B) Hybridization of labeled RNA (single-color) under target limiting conditions for 18, 65 and 140 h. (C) Competitive two-color hybridization of Cy3- and Cy5 labeled RNA mixed at approximately 3∶1 ratio (900 ng and 300 ng, 18 h hybridization). (D) Ratios of signal intensities from competitive hybridization in C. Signal intensities for A and C are normalized to the spot position with the highest signal and error bars for A to D indicate standard deviation per spot position for three replicate hybridizations.