32 transcripts is an optimum threshold for achieving similar cumulative frequency distribution amongst replicates. KS statistics was applied iteratively to our biological replicates (red and black lines), each graph depicts a gradual change in the threshold value. The KS test statistics can be thought of as a cost function that we seek to minimize to ensure that the distributions between the two replicates are similar. Applying such a strategy iteratively as we change the threshold value gradually, we arrive at a point where both line converge together indicating similar distributions. The point where this first occurs is designated as the minimum threshold count value of biological significance.
Koh et al. BMC Genomics 2010 11(Suppl 1):S6 doi:10.1186/1471-2164-11-S1-S6