this is probably a silly question but I prefer to ask...I'm using MACS for peak calling and differential enrichment between two conditions.
I have IgG and my antibody pulldowns in treated and untreated conditions...
intuitively, I should normalize the Ab signal to the IgG signal and then see the difference between treated and untreated conditions...but how can I do this in MACS?
I can get the enrichment of 1) my Ab vs IgG or 2) Ab-no-treatment vs Ab-treatment but in 1) I get the enrichment within the sample and in 2) i don't normalize for IgG
...what are your thoughts?