RnBeads which p-value to use

Question

[a.basitkhan1990]

Hi all,

Which p-value should I use for site based and region based differential methylation analyses, also what is the numerical cutoff of significance for each? Namely: comb.p.val and comb.p.adj.fdr

Thanks!

Answer 1

[ATpoint]

I do not know the package, but generally you always want multiple testing corrected pvalues, commonly called q-values, FDRs or adjusted pvalues. So here one intuitively would go for adj.fdr.

[a.basitkhan1990]

Thank you!