1
$\begingroup$

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?

Improve this question
$\endgroup$
1
  • 1
    $\begingroup$ most likely the data frame is wrangled wrongly. Even the outliers are the same. This is almost impossible $\endgroup$
    – StupidWolf
    Jul 10, 2020 at 12:40

1 Answer 1

Reset to default
1
$\begingroup$

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

Improve this answer
$\endgroup$
1
  • $\begingroup$ Thank you for your feedback @Mariam $\endgroup$
    – M__ ♦
    Jul 13, 2020 at 23:49

Your Answer

By clicking “Post Your Answer”, you agree to our terms of service and acknowledge that you have read and understand our privacy policy and code of conduct.

Not the answer you're looking for? Browse other questions tagged or ask your own question.