A fraction of the input DNA obtained after the sonication step above is labeled with cyanine-5 (Cy5; red) deoxy-cytosine-triphosphate while the methylated DNA, enriched after the immunoprecipitation step, is labeled with cyanine-3 (Cy3; green).  The labeled DNA samples are cohybridized on a 2-channel, high-density genomic microarray to probe for presence and relative quantities.  The purpose of this comparison is to identify sequences that show significant differences in hybridization levels, thereby confirming the sequence of interest is enriched.  
Array-based identification of MeDIP sequences are limited to the array design.  As a result, the resolution is restricted to the probes in the array design.  There are additional standard steps required in signal processing to correct for hybridization issues such as noise, as is the case with most array technologies.
See  for more details.