I have data for 3 histone marks (2 for silencing and 1 for activation) each mark has three replicates.
when I run the
diffBind package I have three contrast:
Silence1-Activation Silence1-Silence2 Silence2-Activation
When I run dba.plotBox for any of contrasts I will have the same distribution of reads.like below: I even tried to start with 1000 peaks of each one that showed higher fold change but again got the same pattern for plotbox. How can I see which peaks belong to which histone marks?