DiffBind, diffferentially binding site 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?
I got the answer from Rory Stark. the samples should have a unique ID. (https://support.bioconductor.org/p/132502/#132514)