I downloaded data using TCGA2STAT across two omics profiles using following code.

library(TCGA2STAT)

seq <- getTCGA(disease="OV", data.type="RNASeq2")

met <- getTCGA(disease="OV", data.type="Methylation", type="all")

seq.met <- OMICSBind(dat1 = seq$dat, dat2 = met$dat) str(seq.met)

1) Download methylation matrix 2) Download expression matrix 3) Filter patients if data not present in both profiles. 4) Normalization of each matrix ?

I would like to know if its correct or not to do normalization after 3 step. As filtering out few patient data will result in un-normalized data points in each matrix. If yes, which normalization method?

Any suggestion will be appreciated

Thanks