Effect of varying Random Forests tree depth on performance. The effect of varying Random Forests tree depth on performance as measured by the distributional deviation of the enrichment P values from the uniform distribution (A) and the percentage of expression traits with a cis-eQTL (B). Smaller node sizes correspond to deeper trees. The permutation importance and RSS importance improve modestly with deeper trees, whereas selection frequency shows more marked improvement with deeper trees. The improvement is measured with respect to forests that stop after the root split (nodesize 114).