Empirical Bayes Model Comparisons for Differential Methylation Analysis

Table 1

Five empirical Bayes models parameter list.

Empirical Bayes model	Parameters	Observed data	Missing data
BGG	𝑎,𝑎0,𝜈,𝑝	𝑦𝑖𝑗𝑘	𝑧𝑖
BNGG	𝑎,𝑎0,𝜈,𝜏𝑖,𝑝	𝑦𝑖𝑗𝑘	𝑧𝑖
BNNGG	𝑎,𝑎0,𝜈,𝜏𝑖,𝑝	𝑦𝑖𝑗𝑘,𝜎𝑖𝑗𝑘	𝑧𝑖
BLNN	𝜇,𝜑,𝜏𝑖,𝑝	𝑦^′𝑖𝑗𝑘	𝑧𝑖
BLNNN	𝜇,𝜑,𝜏𝑖,𝑝	𝑦^′𝑖𝑗𝑘,𝜎^′𝑖𝑗𝑘	𝑧𝑖

Note: 𝑖, 𝑗 and 𝑘 represent probe, sample and replicate, respectively.