I have DNA methylation results obtained using the methylKit tool, controlling for age, sex, batch effects, cell heterogeneity, and PCA. Total CpGs = 1,597,844, with the following counts of significant results:
• DMPs with significant p-values (without filtration): 64,169 • Significant FDR: 11,091 • Significant FWE: 1,795
When I attempted to create a Manhattan plot using all CpGs, the plot appeared unusual because many DMPs were above the significance level of 5e-8. However, when I plotted the top 27 significant DMPs, their significance threshold was 1e-40. what do you think
Which results are better to use for the Manhattan plot? Additionally, should I filter the results according to methylation difference first before performing multiple correction?
