I used macs 1.4 and macs 2 for peak calling. Then I used Homer (anonotatePeaks.pl) for peak annotation to hg19. Peak scores ranges from 3205.08 to 50 and 342.34 to 2 respectively. The number of peaks identified are 65229 and 74979 respectively. I used the default parameters in both cases. Why is there so much variation in peak scores? what is the role of this peak score ? It is not clear from the Homer website.
High peak score means that there are more chances of true positive peak? If yes, then what could be the right threshold to filter out the peaks?
In the supplementary material of a paper I found the information that they used Homer for chip-seq peaks identification and filter the peaks by peak score >10, but there they are not mentioning a reason behind this threshold.