I have managed to create a GenomicRatioSet (minfi object) from an expression set (pulled from GEO using GEOquery) which contains a matrix of pre-processed beta values obtained with the exprs() function as such:

GRset <- makeGenomicRatioSetFromMatrix(exprs(Eset), 
rownames = rownames(exprs(Eset)), 
pData = pData(Eset),
array = "IlluminaHumanMethylation450k",
annotation = "ilmn12.hg19",
mergeManifest = TRUE, 
what = "Beta")

I have found working from pre-processed data quite difficult as it doesn't come in the form/object that minfi wants it and I couldn't find a way to incorporate the Manifest and annotation but this seems to have worked with the above. My issue now is that I would prefer to have a more recent genome annotation. I have only managed to find this https://zwdzwd.github.io/InfiniumAnnotation
How could I annotate this data with a more recent gene set from e.g. Ensemble

Cheers