TCGA methylation analysis

Question

[ali]

Hi everybody,

I hope you are all doing well.

Does anyone know how to analyze TCGA methylation data? I have viewed some pipelines, but I got confused.

query_met <- GDCquery(project= "TCGA-BLCA", data.category = "DNA Methylation", platform = "Illumina Human Methylation 450", data.type = "Methylation Beta Value")

GDCdownload(query_met,method = "api",directory ="" )

putting files together

data.met <- GDCprepare(query_met,directory = "",summarizedExperiment = T)

Up until this point, I haven't encountered any issues, but beyond this stage, I’m unsure which package or pipeline should be used for normalization and DMSs.

Thanks