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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 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?

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    $\begingroup$ most likely the data frame is wrangled wrongly. Even the outliers are the same. This is almost impossible $\endgroup$
    – StupidWolf
    Jul 10 '20 at 12:40
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I got the answer from Rory Stark. the samples should have a unique ID. (https://support.bioconductor.org/p/132502/#132514)

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  • $\begingroup$ Thank you for your feedback @Mariam $\endgroup$
    – M__
    Jul 13 '20 at 23:49

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