There is an estimateCellCounts() function in minfi. One of the parameters is returnAll which returns normalized user supplied data. That is returning quantile-normalized values that were normalized along with the reference dataset. Is there a way to get values adjusted by cell-type composition?

There is a estimateCellCounts Visualisations - Adjusting Beta Values for Plotting from about 2 years ago that seems to suggest there is not really a good solution to that problem. I don't know if there have been any developments since then.

There is also another package celltypes450 that attempts to adjust the beta values. However, since that hasn't been implemented in the minfi version, I am concerned.