I'm new in ChiP-seq analysis. I'm using SICER to analyze histone modification data with a control library. I have some doubts regarding the output file. In the output file (summary of filtered islands with an FDR < 0,01) there are some peaks which appear to be more enriched in the control library respect to the chip one. Is it normal? I thought I would have peaks only enriched in chip library. How is the fold change value calculated? Does it exist a best used threashold to filter this value?