Hi,

I'm using the Combat function to correct for the batch effect as my main approach. and for the sensitivity analysis, I used SVA function.

When I used Combat, my model showed no significant result between baseline and follow-up methylation measurements. When I used SVA, one CpG site showed a significant difference.

I would like to know what is the difference between the two approaches and I'm trying to find the limitation for the two

if someone can suggest articles and resources that will be appreciated