The percentage of transcripts reported differentially expressed, FPR defined by Eq. 4 by three software packages for synthetic data generated under the null hypothesis of no DE between two conditions. In the lower two panels the set of transcripts has been divided into those with greater than 100 counts (DE-high) and those with less than or equal to 100 counts (DE-low) averaged over biological replicates. The number of biological replicates in each condition was varied over the range n = 2, 3, …12. The experiment was repeated for 100 independently generated datasets. The top of each bar is the median value obtained and its 90% confidence interval.