would you please advise, shall we do a comparison between two different ChIP-seq datasets,
that have been generated in two cell lines,
for example, H3K4me3 in HEK293 and H34me3 in IMR90,
in order to show that the data in HEK293 is better than in IMR60, which metrics would you choose ?
To keep in mind that the loci marked by H3K4me3 in HEK293 is very different than the sets of loci marked by H3K4me3 in IMR90.
Thanks a lot,