P value distributions by gene read count quantiles from null model evaluations. Null model comparison where differential expression (DE) is evaluated between samples from the same condition is expected to generate a uniform distribution of P values. Indeed, the P value density plots, stratified by read count quartiles, have a uniform distribution. However, at the common significance range of ≤ 0.05 there is a noticeable increase in P value densities in Cuffdiff results indicating larger than expected false DE genes. The smoothing bandwidth was fixed at 0.0065 for all density plots and 25% was the lowest gene read count quartile.
Rapaport et al. Genome Biology 2013 14:R95 doi:10.1186/gb-2013-14-9-r95