I am trying to incorporate Methylation data (Illumina 450K) into my pipeline. I was provided with two versions of the same data: one (dataset $a$) normalized with ComBat and the other (dataset $b$) normalized using the residuals method (i.e., taking the residuals of the models fitted on the covariates). Looking at the distribution of the beta values, I noticed that:
- The values for dataset $a$ have a typical bimodal distribution with peaks at around $0$ and $1$
- The values for dataset $b$ are roughly normally distributed with the mean at around $0.5$.
I am not that familiar with Methylation data, so maybe this is expected. Is it? I did not find any paper showing similar results.