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RStudio Diffbind analysis shows no result

Hi all, I'm trying to carry out a differential accessibility analysis on ATAC-seq data using DiffBind. I'm reading in a .csv file as my sample sheet and getting a decent correlation heatmap per the instructions in section 3.1 of the DiffBind manual. However, when I carry out dba.count(), I get "Error: No sites have activity greater than filter value." The same dataset that gave me thousands of differentially accessible sites when I ran a quick analysis on Galaxy, but I'm getting nothing here. Would anyone have an idea of what I could modify in these early stages of the analysis pipeline to address this issue? Thanks in advance.

galaxy diffbind rstudio
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updated by Ram Ram • written by a_bis • a_bis

Let me kindly suggest to google "Error: No sites have activity greater than filter value." and you will find previous answers on that.

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written by ATpoint ATpoint

Thank you for your kind suggestion. I have indeed googled this in an effort to resolve the question, and found what appears to be a useful post on bioconductor (https://support.bioconductor.org/p/9137594/). It suggests running dba.peakset(samples, bRetrieve=TRUE) to look at the matrix after reading in the samples and before counting, but I seem to be getting Error in rep(T, nrow(pv$binding)) : invalid 'times' argument. Unfortunately I can't identify what this times argument refers to as I don't know where the rep() comes in play.

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updated by Ram Ram • written by a_bis • a_bis

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