The smoothed Y statistic is far elevated from limma Y statistic, and parameter "betacutoff" never used
0
0
Entering edit mode
zh9118 • 0
@zh9118-21668
Last seen 8 months ago

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

dmrcate • 111 views
ADD COMMENT
0
Entering edit mode

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
0
Entering edit mode

Hi Tim,

Thanks for the explanation.

Hua

ADD REPLY

Login before adding your answer.

Traffic: 546 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6