Figure 4
POG at different percentages of genes selected as significant with three gene selection methods. In both cases (with or without data filtering), p-value ranking resulted in much lower cross-platform concordance compared to fold-change and SAM, in particular when a small percentage (e.g., <20%) of candidate genes are selected as significant, suggesting that the most significant genes selected by p-value ranking from one platform are unlikely to be selected as significant from another platform. POG by chance (assuming no correlation in log ratios, i.e., LRr2 = 0 among the three platforms) is also shown. See Figure 6 for more information on POG by chance.