Hi Michael Love

I was trying to follow your workflow as described here for DTU analysis I am confused, if the below code chunk is trying to fish out the intersection of genes obtained from DTU, DEU and DEG and that dte.genes and dtu.genes are the geneset obtained after their respective StageR steps? Source:here

Also, why did you mentioned # we can only color because we simulated...

This is the part of the code that only works for the simulation data, hence "we can only color because we simulated".

In simulation, we have access to the true status of the gene (whether it is DGE, DTE or DTU as defined in the publication). But you won't have that with your own data.