Figure 1

MA plots and volcano plots showing data from the linear model fitted to replicate arrays for each of the DMH-v1, DMH-v2, MMASS-v1, MMASS-v2, and MeDIP methods. Colored probes represent external DNA controls, Hex, Alien PCR product, DMSO, empty, and blank, respectively. The results of external DNA controls are nearly consistent with theoretical ratios. Plots of MMASS with either v1 or v2 set of enzymes show higher M, B values and Log₂fold change than DMH and MeDIP methods.