Figure 2

Simulation of different biological samples. We consider biological samples with very different characteristics in order to confirm that the protocol assessment is independent of the particular samples used for calibration. The pie charts in the second column of this figure show the varying distributions of differential expression examined. They were obtained by randomly selecting different proportions of genes with zero, low, medium, or high differential expression (Z/L/M/H) from the original measurements. The performance of the competing protocols (A... E) is quantitatively assessed and ranked for each simulation, represented by the rows in the second column. The distribution of ranks (third column) then indicates to what degree the obtained ranking is independent of the samples used for calibration. A stable ranking means that the found optimum will equally apply to arbitrary future measurements. In the example illustrated here, the optimum 'C' was robustly ranked first, whereas the protocols 'A' and 'B' as well as 'D' and 'E' show similar average performances. The optimum 'C' was therefore reliably identified.