Hello, everyone. I searched in ENCODE for ChIP-Seq experiments and visualized them in UCSC browser. For instance, I searched for TATA-box binding protein (TBP) assays and went to FOS' promoter to examine its TBP peaks.
I kind-of get the idea of optimal Irreproducible Discovery Rate (IDR) for the peaks, but I don't really understand the measure of "fold change over controls" that UCSC gives you along the optimal IDR. Correct me if I'm wrong, but in the ChIP-Seq experiments' metadata (from ENCODE) it was stated that there was no perturbation (no treatment, no illness, nothing) in the samples, which makes me think those are the controls. If that's the case, then what exactly do they mean with "FC over controls", if the peaks are comming from "control" samples?