I got puzzled by the peaks called by MACS14 peak caller. Attached is the image where black bar on the top of peaks represent that the peak is significant (peaks file from Macs). I observe significant peaks in the 2nd and the 3rd track but not in the first one though the enrichment (height of the peak) is two-fold more as compared to other, 74 vs 46 and 37.
What could be the reasons, I ran peak caller twice to double check with different bandwidth (250,300), I get same list of peaks. Also, the control used for peak calling is an Mock-IP control with 10 Mil reads where as samples has around 20-22 Mil reads. Macs is doing the inbuilt read normalization (Small dataset will be scaled towards larger dataset.).
How can I confirm its true or not, if true then what are the possible causes.
Thanks for your input.