<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>

CC BY-SA 4.0
2020-07-13T23:49:20.647Z
Thank you for your feedback @Mariam
M__
CC BY-SA 4.0
2020-07-13T20:22:15.307Z
2020-07-13T20:22:15.307Z
Mariam
<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>

CC BY-SA 4.0
2020-07-10T12:40:14.453Z
most likely the data frame is wrangled wrongly. Even the outliers are the same. This is almost impossible
StupidWolf
<phylogenetics><bioconductor><sequence-analysis><chip-seq>
DiffBind, diffferentially binding site
# 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:

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 @Mariam  

---

