I am trying to combine raw (.idat) and GEO (intensity matrix) Illumina 450K data sets using minfi.
geo.data <- getGenomicRatioSetFromGEO(GSE="")
targets < read.450k.sheet("my.data.csv")
my.data <- read.450k.exp(base="data", targets=targets)
my.data.raw <- preprocessRaw(my.data)
my.data.RG <- ratioConvert(my.data.raw, what = "both")
my.data.mset <- mapToGenome(my.data.RG)
At this point, is there a way I can combine the two GenomicRatioSets to form a single data set for downstream analysis? Sorry if this is a basic question, but I havn't been able to figure it out.