Hello! TIA for helping =)

so via DiffBind, I import a SampleSheet:

SS <- DiffBind::dba(sampleSheet = csvFile, scoreCol = 5)

The sample sheet has 6 bed files, 3 replicates of one sample and 3 replicates of a second sample.

I made the venn diagram:

Venn <- DiffBind::dba.plotVenn(SS, 1:3)

everything works great and I get the number of peaks that overlap between the first 3 replicates.

However, if I go back to the original sample sheet and add three more replicates (of another sample) to the csv file (now total of 9 bed files), and then go ahead and create the DBA file, and plot Venn <- DiffBind::dba.plotVenn(SS, 1:3) again, the numbers of overlap change a little (approximately a difference of about 60 peaks).

My concern is that I only made the venn diagram from the first three replicates, both times, and the number of peaks slightly changed, when i added more bed files to the csv.

Thank you!