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why DiffBind, diffferentially binding site is the for different samples

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 enter image description here

I even tried to start with 1000 peaks of each one that showed higher fold change but again got the same pattern for plotbox. Even the outliers are the same, How it's possible?

here is the code:

peaks10kthreemarksobj <- dba(sampleSheet="samplesheets10kPeaks.csv") peaks10kthreemarksobj <- dba.count(peaks10kthreemarksobj, bUseSummarizeOverlaps=TRUE,bParallel=TRUE) peaks10kthreemarksobj <- dba.contrast(peaks10kthreemarksobj, categories=DBAFACTOR) peaks10kthreemarksobj <- dba.analyze(peaks10kthreemarksobj, method=DBAALLMETHODS, bParallel=T) dba.plotBox(peaks10kthreemarksobj, contrast=3)

chip-seq alignment diffbind
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updated by Rory Stark Rory Stark • written by iridha • iridha

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See reply at https://support.bioconductor.org/p/132502/#132509

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written by Rory Stark Rory Stark

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