The smoothed Y statistic is far elevated from limma Y statistic, and parameter "betacutoff" never used

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zh9118 • 0

@zh9118-21668

Last seen 8 months ago

United States

Hi there,

I have two questions about DMRcate:

1) Why the smoothed Y statistic (SKY) is far elevated from limma Y statistic? extracted the SKY from the code. 2) From the code, the parameter "betacutoff" has never been used. Is it?

Thanks, Hua

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ADD COMMENT • link 4.4 years ago zh9118 • 0

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Hi Hua,

1) Yes that's right - this is normal for kernel aggregation given it's a local sum. Remember that SKY is moderated by SK and S_KK using Satterthwaite, and also the FDR is indexed against the number of DMLs - both control for this inflation.

2) Thanks for spotting - that filter must have been squelched a few updated ago. I've put it back in: https://github.com/timpeters82/DMRcate-devel/blob/master/R/dmrcate.R#L176-L180.

Cheers, Tim

ADD REPLY • link 4.4 years ago Tim Peters ▴ 200

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Hi Tim,

Thanks for the explanation.

Hua

ADD REPLY • link 4.4 years ago zh9118 • 0

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