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RnBeads which p-value to use

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!

methylation rnbeads
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updated by ATpoint ATpoint • written by a.basitkhan1990 • a.basitkhan1990

1 answer

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.

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written by ATpoint ATpoint

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