Resolution:
## Figure 3.
. Null model comparison where differential expression (DE) is evaluated between samples
from the same condition is expected to generate a uniform distribution of P value distributions by gene read count quantiles from null model evaluationsP 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 |