I have an output file from Genome studio that has not been normalized. I want to apply the functional normalization method found in the minfi package to my methylation data but I don't have access to the IDAT files only the Genome studio output file. I found an internal method in the minfi package that reads the data from Genome studio in (read.GenomeStudio) but that doesn't result in a rgSet which the functional normalization method requires to work. Is there some critical information in the IDAT files that makes this impossible or can I somehow cast my GenomeStudio data to an rgSet?
TL;DR is there any way to apply functional normalization from the minfi package to a Genome studio output file from Illumina 450k?