Dear Bioconductor community,

I am interested in using DiffBind. I am following the procedure in "DiffBind: Differential binding analysis of ChIP-Seq peak data" and I got a bit confused, I hope you can help me. 

My first question is a bit general, if I understand correctly DiffBind from the very beggining (reading the peaksets) only takes into account the peaks that are merged (shared) between all the samples. So if there were two expeimental conditions and two replicates per condition and a peak was consistently found in the two condition1 replicates but not in the replicates for condition2, this peak would not be taken into account, is that correct?

 My second question is in the "Deriving consensus peaksets" part,in page 20, the line says:

"Alternatively, a master consensus peakset could be generated, and reads counted, directly using dba.count: tamoxifen
<- dba.count(tamoxifen, peaks=tamoxifen$masks$Consensus)"

if I try this I receive the next error:

"Error in pv.counts(DBA, peaks = peaks, minOverlap = minOverlap, defaultScore = score,  :
  Can't count: some peaksets are not associated with a .bam file."

I have my consensus peak lines (replicates) in the dba object but there are no BAM files associated in the original "sampleSheet". Would you recomend to merge the BAM files and upload a new sample sheet?

Thank you for your time and your attention,

Regards,

Hi,

In regard to your first question, you can control how many peak sets have to include a peak for it to be included in the analysis.  In both dba and dba.count, the parameter minOverlap controls this: if for example you supply the argument minOverlap=2, then any peak that occurs in at least 2 peak sets will be included.

I'll have to leave the second part to Rory... I don't really understand what he is (or you are) trying to accomplish there.

Cheers,

 - Gord