Normalization of the WGBS smooth data about bsseq HOT 5 OPEN

Hi,
I am finding methylation signal low in some of the my samples and suspecting batch effect and want to normalize the smooth beta values (returned after getMeth() function). Want to feed this matrix into the object again but as bsseq object does not keep smoothed matrix directly. It looks to me it keep coef matrix which transform in smooth data. So I am unable to find the way where I can replace my smooth methylated profile/matrix with normalize smooth profile as I want to feed this object file in the DMRcate tool to identify DMRs.
Looking forward for suggestions.
Thank you,
Priya

from bsseq.

I've never done any normalization of the data following smoothing.
@kasperdanielhansen have you?

As you note, the BSseq object does not contain the smoothed values, only the parameters, but the smoothed values can be obtained with getMeth().
I don't know how DMRcate works, but perhaps there's a way to pass in (normalized) values of getMeth() as input rather than a BSseq object to the DMRcate functions you want to use?
That's a question for the developers of that package.

from bsseq.

from bsseq.

Thank you for considering my question. I have visualized a DMR region of the smooth data and suspecting the batch effect. I want to identify drms using the smooth quantile normalized data with DMRcate as I have many covariates.
I checked DMRcate uses bsseq object not any data frame/matrix.

Here is the screenshot I am sending for understanding..

Thank you for any help and suggestions.
Priya

from bsseq.

Sorry, I don't understand what you're trying to show with that screenshot.

from bsseq.