Hi! I have 9 samples (each condition has three samples). I am running diffbind as follows:

dbind<-dba(sampleSheet = "diffbind.csv")
dbind_consensus <- dba.peakset(dbind, consensus=c(DBA_TISSUE,DBA_CONDITION),minOverlap=0.66)
dbind_consensus<-dba(dbind_consensus, mask = dbind_consensus$masks$Consensus,minOverlap = 3)

After this runs I get the following warning:

All peaksets unique for specified attributes; no consensus peaksets added.

And I get the following error:

Error in sum(supply(peaks, nrow)) : invalid 'type' (list) of argument
Calls: dba -> pv.model -> pv.vectors

Do you have any suggestions? Thanks!

I'm thinking that the call to dba.peakset() results in only one (or even zero) consensus peaksets being added? This would be the case if there was only one unique combination of Tissue/Condition values. It should print out all the consensus peaksets being added, how many were there?

If you send me a a copy of the DBA object, I can tell you for sure what is happening.