I have a bit of an odd question which admittedly has come more from my PI than me.
We have done some ChIP-seq analysis for a TF on some tissue and cell samples. I have analysed all of these samples with the exact same pipeline and for each sample, I have run MACS2 to identify peaks against an input control for each sample. What I want know is, is it fair to say if I have more peaks called in one sample versus another cell sample that the sample with higher peak number has more TF binding to DNA than the other sample? For example, I have sample A with 3900 peaks, sample B with 11000 peaks and sample C with 19000 peaks. In order to say that my sample C has more TF binding to the DNA than the other samples, is there any sort of normalisation I should do? Are these numbers comparable to each other as is? I've read a lot about normalising peak heights between samples (using library size etc) but this is a different question. Can numbers of peaks themselves be compared between samples??