text: user8543: 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?
  
  user8543: I got the answer from Rory Stark. the samples should have a unique ID. (https://support.bioconductor.org/p/132502/#132514)
  
original_text: 8543: <p>I have data for 3 histone marks (2 for silencing and 1 for activation) each mark has three replicates.</p>
  <p>when I run the <code>diffBind</code> package I have three contrast:</p>
  <pre><code>Silence1-Activation
  Silence1-Silence2
  Silence2-Activation
  </code></pre>
  <p>When I run dba.plotBox for any of contrasts I will have the same distribution of reads.like below:
  <a href="https://i.stack.imgur.com/wchgv.png" rel="nofollow noreferrer"><img src="https://i.stack.imgur.com/wchgv.png" alt="plotBox" /></a>
  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?</p>
   8543: <p>I got the answer from Rory Stark. the samples should have a unique ID. (<a href="https://support.bioconductor.org/p/132502/#132514" rel="nofollow noreferrer">https://support.bioconductor.org/p/132502/#132514</a>)</p>
  