To count differentially-methylated promoters that supported variance due to cellular origin or genetic background, within-sample methylation difference was compared to the between-sample methylation difference for each promoter in sets based on cellular origin (hESC/hiPSC) and cell background (HUES2/HUES3). The promoter was assigned to the set with the lesser methylation difference, such that promoters in the hESC/hiPSC set showed greater methylation difference between hESCs and hiPSCs and lesser metylation difference between HUES2 and HUES3.
