My first question is, what is the standard measure of FDR (if any) while calling peaks in ChIP-Seq.
And, how to co-relate the emperical FDR from Macs14 (peak caller) to a q-value threshold.
Is it just,
empFDR=(q-value/10)*100 or one cannot make such remarks.
Can we modulate this threshold on the case to case basis. There might be a case, when your protein is low expressed, so the enrichment is low. And when you call peaks, they pass the p-value threshold, but the enrichment at most postions is same or less than the control, so FDR is high. What to do in that case.
P.S. The empirical FDR in Macs 14 is defined as Number of control peaks / Number of ChIP peaks.