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.