I did the protocol as Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks from the nature protocol. The online pdf is here
I have a question when i see Figure 8, as below,
I find the boundary between sig and no sig is around 2.5 on the left axis, its p-value is about 0.003. But i think it should be 2(p-value 0.01) or 1.3(p-value 0.05) on the axis.
I am confused by this figure and need some help.