Answers.Body: <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>
  
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Answers.CreationDate: 2020-07-13T23:49:20.647Z
Answers.Text: Thank you for your feedback @Mariam
Answers.UserDisplayName: M__
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-07-13T20:22:15.307Z
Answers.LastActivityDate: 2020-07-13T20:22:15.307Z
Answers.UserDisplayName: Mariam
Body: <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.sstatic.net/wchgv.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/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>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-07-10T12:40:14.453Z
Comments.Text: most likely the data frame is wrangled wrongly. Even the outliers are the same. This is almost impossible
Comments.UserDisplayName: StupidWolf
Tags: <phylogenetics><bioconductor><sequence-analysis><chip-seq>
Title: DiffBind, diffferentially binding site
ThreadText: # DiffBind, diffferentially binding site
  
  (Asked by: username_0 on 2020-07-10)
  
  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:
  [![plotBox](https://i.sstatic.net/wchgv.png)](https://i.sstatic.net/wchgv.png)
  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?
  
  **Tags:** phylogenetics, bioconductor, sequence-analysis, chip-seq
  
  > **Comments:**
  > **username_1**: most likely the data frame is wrangled wrongly. Even the outliers are the same. This is almost impossible  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_0 on 2020-07-13. Score: 1
  
  I got the answer from Rory Stark. the samples should have a unique ID. (<https://support.bioconductor.org/p/132502/#132514>)
  
  > **Comments:**
  > **username_2**: Thank you for your feedback @username_0  
  
  ---
  
  