Firstly, I'm relatively new to R and methylation data.
I'd like to analyze this geo dataset (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE21232). It is performed with Human Methylation27 DNA BeadChip arrays. The data only provide beta-values (no A- and B-values). I know how to perform the analysis with lumi once I have a MethyLumiM object in R. But I'm not able to get there.
I followed this manual about GEOquery (https://bioconductor.org/packages/release/bioc/vignettes/GEOquery/inst/doc/GEOquery.html) and was able to create an ExpressionSet (without the annotation library). However, I do not know how to proceed.
Any help will be greatly appreciated. Thank you!