I use the function dba.report to retrieve differentially bound sites (th = 1) I found the fold-changes tend to be very small and do not know how to compute them.
For example, at one site the mean for control is 1.6973 while the mean for treatment is 4.231, and the Fold is -0.001057009, p-value is 0.0051515283, FDR = 0.99.
How the fold-changes were computed? my code is below.
cond = "treatment" obj = dba(sampleSheet=data0) obj = dba.count(obj,minOverlap=2) obj = dba.normalize(obj,normalize=DBA_NORM_RLE,library=DBA_LIBSIZE_PEAKREADS) obj = dba.contrast(obj,reorderMeta=list(Condition=cond),minMembers=2) obj = dba.analyze(obj) dbp = dba.report(obj,th=1)
I used DiffBind v3.10.0.
According to https://www.biostars.org/p/9467075/