Hi all, I am trying to use DiffBind to compare peaks called in control vs condition. I have 2 replicates for each and I've also called peaks using 2 different peak callers (to wi, MACS and QuEST). I've also prepared a sample data sheet that looks like this: SampleID Tissue Factor Condition Replicate Peak.caller bamReads bamControl Peaks control Hela TF wt 1 MACS path path path control Hela TF wt 1 QuEST path path path control2 Hela TF wt 2 MACS path path path control 2 Hela TF wt 2 QuEST path path path (and the same for the conditions) My plan was to load all the data and then using diffbind selecte a set of common peaks for the peak callers before proceeding with the analysis. However, when I load the data (data = dba(sampleSheet="samplesheet.csv")) the peaks for each caller are not recognized as a different variable. How I can do that and is this silly? I could also derive a set of common peaks independently but it would be neat to do it all with the same package and that seems to be possible but I could not find how to do it in the documentation. Thanks, António -- -- António Miguel de Jesus Domingues, PhD Neugebauer group Max Planck Institute of Molecular Cell Biology and Genetics, Dresden Pfotenhauerstrasse 108 01307 Dresden Germany e-mail: domingue@mpi-cbg.de tel. +49 351 210 2481 The Unbearable Lightness of Molecular Biology [[alternative HTML version deleted]]