Hi, 

I am having some trouble with the dba.count function in Diffbind dba.count function. See below: 

DBA.count = dba.count(DBA, bUseSummarizeOverlaps = FALSE, mapQCth = 30, bCorPlot = FALSE, bParallel = TRUE, minOverlap = 2)
Error in pv.counts(DBA, peaks = peaks, minOverlap = minOverlap, defaultScore = score,  : 
  Can't count: some peaksets are not associated with a .bam file.

It previously worked on the same dataset doesn't seem to work anymore. 

Please help

This error arises when there is no bam file specified for a peakset. Check your sample sheet to ensure that there is a column named bamReads (case sensitive). you can check how your samplesheet looks after processing as follows:

> DBA$samples

You can also check all the bam file paths as follows:

> DBA$class[10,]