Do people use M-value in WGBS?

Question

[Woobin]

Hi all,

I have one question about M-value.

I have seen that many people used M-value in microarray anaylsis instead of beta-value.

I was wondering that the M-value is available in methylation sequencing such as WGBS.

Thank you.

Answer 1

[Papyrus]

The thing is that for arrays, the DNAm measurements come from kind of a continuous signal which has a lot of heteroskedasticity and the logit transformation to M-values is often used in the field because many pipelines use statistical methods which benefit from this. For sequencing methods, the origin of the data is quite different (read counts) and different tools require different inputs, in general most require counts or methylation percentage computed from the counts, because they model the data differently, but it will depend on the tool.

[Woobin]

Thank you! Your reply is helpful.