I have performed a differential methylation analysis using MEDIPS (R Bioconductor package) using data from 2 types of cells to identify regions which are methylated in one but not in the other (or hypermethylated in one and hypomethylated in the other). For each cell type, I had 3 replicates and then I separated the regions obtained according to the log fold change (if it was positive I assigned that to one cell type and if it was negative to the other).
However, after performing the analysis, I obtained some regions which appear to be methylated in both. More exactly, I have intersected the regions obtained with gene coordinates and one gene appears in both sets.
Does anybody have any idea why I obtained the same gene after performing differential methylation analysis for genomic regions which are differentially methylated in each of the cell types?