I have been using DiffBind to perform differential binding analysis on ChIP-seq data, comparing two groups with 3 replicates for each. I am now facing an error when using its dba.count function.
I created a DBA object, Expt, using a sample sheet.
Expt <- dba(sampleSheet=”Expt.csv”)
After creating consensus peaksets by
Expt <- dba.peakset(Expt, consensus = -DBA_REPLICATE)
I used the dba.count function as follows.
Expt <- dba.count(Expt, peaks=Expt$masks$Consensus)
I then got an error message as follows.
Error in pv.counts(DBA, peaks = peaks, minOverlap = minOverlap,defaultScore = score,
Can’t count: some peaksets are not associated with a .bam file.
What is weird is that, when I used dba.count function on all the samples, without creating consensus peaksets, it works without showing any error message. In addition, this error message did not appear, when I used an older version of DiffBind. This error happens after I have updated R to ver. 3.3.1 and downloaded the latest version of DiffBind.
Thank you so much.