Figure 5

Rank distributions of different hybridization protocols. Pie charts illustrate the rank distributions of competing protocols from performance comparisons for 100 gene subsets that correspond to samples of different properties. Every subset was used for evaluating all eight protocols to obtain a ranking (see schema in Fig. 2). While some random variation between the observed protocol rankings must be expected, in 90% of all tests the hybridization temperature of 51°C performed best, with the remaining 10% split between the two 50°C hybridizations ('50a', '50b'). This verified the reliability of the original calibration. The remaining ranking was also very stable, with a larger uncertainty, as expected, only seen for the two hybridizations at 50°C. The high similarity of the two 50°C measurements further confirmed the reproducibility of the calibration process. In summary, the obtained ranking and, in particular, the obtained calibration optimum were robust and independent of the biological samples used for calibration.