To practice we are going to be working with the RA data again to investigate associations with global, site-specific, and regional changes in methylation. I have created a workflow here. Below are some follow-up questions to explore.
How does adjusting for batch impact these results? You can try this multiple ways.
How does adjusting for cell distribution impact the results? Was this expected?
If you detect any regional changes, where are they occurring? Try to plot the differentially methylated region.