Hi

 

 

dmpFinder uses beta-values for fetching the differentially methylated
positions. I would like to know if using the SWAN normalized M-values can be
used for the same? And, if that's a suitable approach, how to go about it
(convert the M-vales to beta-values and then perform dmpFinder on these
values; does it require logit transform as well)? 

 

I have actually run dmpFinder on the M-values, post SWAN normalization
(without any conversion to beta values or without any transformation), and
like the previous post, I would like to know the methylation status of the
differential positions, but am unsure about the approach to be taken for the
same. And all the same, I am unable to understand whether the value of
intercept should be of any concern to me..

 

Kindly help!!

 

Thanks in advance


	[[alternative HTML version deleted]]

