Figure 1

Mulcom optimization plot. Optimization plot generated by Mulcom to choose test parameters (m and t). The heatmap highlights the number of significant genes for each combination of m (y-axis) and t (x-axis) with a FDR below the threshold defined by the user (five percent in this case). Given the FDR threshold of choice, the box with the colour closest to the top of the scale indicates t and m values giving the maximum number of significant genes. Additional boxes to the right and top of the lightest one are shown to provide an estimate of the number of significant genes passing the test under more stringent t and m conditions. Whether such conditions further improve FDR, should be tested by fixing a lower FDR threshold and repeating the analysis.