HI there!

i am working with 100 sample of  850K methylation data. After probe filter and normalization, SVD plot indicate that batch effect (including slide and array) has an impact in methylation status. Unfortunately, Slide is confounded with SampleGroup (the factor of our interest). So i cannot use Combat to correct the batch effect as usual. 

Then I found missMethyl package provides ruvfit/ruvadj to correct the unwanted variation. The documentation says  RUV estimate the component of unwanted variation using negative control probes (INCs) that are known a priori to not truly be associated with the biological factor of interest, but are affected by unwanted variation. And in the PCA plot of INCs in my data, INCs are clustered by Slides. It seems ruv fits for use in my data.

what troubles me is that except differentially methylated probes, i also need a matrix of methylation value, which already corrected for batch effect,  for further analysis. But I don't find a value to represent methylation status in the output of ruvfit and ruvadj.

Could someone suggest to me how I could get a matrix of unwanted variation corrected methylation value? 

Thank you !