Figure 3.

Scatter plots of algorithm performance rank order versus agreement of paired PBMs. A, B, C, and D show scatter plots of algorithm performance rank order versus the length of the major axis of the PCA ellipse (i.e. 99.73% limit of PCA quality-control ellipse), the length of the minor axis of the PCA ellipse, correlation coefficient of normalized 8-mer median intensities between a pair of training and testing PBM experiments, and regression coefficients, respectively. Both PCA ellipse and regression coefficient are based on scatter plots of Z-score transformed 8-mer median intensities between a pair of training and testing PBM experiments. In the figure, the black smooth lines are fitted linear regression lines to the scatter plots, and the P-values of the regression lines are indicated at the top of each figure. The rank order of TFs (i.e. 66 TFs were sorted in decreasing order by mean final algorithm performance scores) is adopted from Figure 2 of the DREAM5 challenge paper.