I am using DiffBind to analysis some hMeDIP-seq data. I have called peak from MACS2 (narrow) and SICER (broad) separately. And the results can both be loaded into DiffBind. I like to generate AffinifyBinding matrix for custom downstream analysis and visualisation, as it returns nice coordinates format and normalised peak intensity value.
My question is, I can't comapre the two peak value matrixes (from AffinityBinding matrix) between narrow/broad peaks right? Since they are from different peak-caller. For example, I can't find genes have higher peak signal in gene body than gene promoter.