TCGA methylation analysis
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
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