Scatter plot and confusion matrix. (Left) The scatter plot shows the correlation between prediction scores (x-axis) and true log expression values (y-axis) for genes on held-out experiments. (Right) Confusion matrix: truth and predictions for all genes in the held-out experiments, including those expressed at baseline levels. Examples are binned by assigning a threshold of 0.95 for positive prediction scores and -0.2 for negative prediction scores.
Kundaje et al. BMC Bioinformatics 2006 7(Suppl 1):S5 doi:10.1186/1471-2105-7-S1-S5