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After correct preprocessing of the data (i.e. filtering out problematic probes and normalizing the data), differential methylation analysis can be performed. Generally, the first approach consists in a single-probe analysis. Statistical tests (such as the t-test or Mann–Whitney test) are used, and when the P-values obtained are below a given threshold (e.g. <0.05), the sites are considered as differentially methylated and referred as differentially methylated positions (DMPs). In this way, several researchers have identified numerous DMPs although the absolute difference in methylation of the CpG sites between two groups of samples was small (i.e. below 5% of methylation difference).
(Dedeurwaerder et al., 2014) A comprehensive overview of Infinium HumanMethylation450 data processing. Brief Bioinform.