Stability of logarithmic fold changes. DESeq2 is run on equally split halves of the data of Bottomly et al. , and the LFCs from the halves are plotted against each other. (A) MLEs, i.e., without LFC shrinkage. (B) MAP estimates, i.e., with shrinkage. Points in the top left and bottom right quadrants indicate genes with a change of sign of LFC. Red points indicate genes with adjusted P value <0.1. The legend displays the root-mean-square error of the estimates in group I compared to those in group II. LFC, logarithmic fold change; MAP, maximum a posteriori; MLE, maximum-likelihood estimate; RMSE, root-mean-square error.