How to normalized the different cancers of Level 3 TCGA data of DNA Methylation

Question

[sheny]

Hi, I just found different tumor-specific working groups may do the job differently. So although the level 3 data of each cancer on DNA methylation (450K) has been normalized, if I want to put the different types of cancer together, I still need to normalized again. My question is how to deal with these beta values?

[sheny]

Anybody knows how to normalize the beta distributed data. Thanks

[sheny]

Thanks so much. It is useful

Answer 1

[Shicheng Guo]

Actually, you can use quantile normalization to deal with this problem.

library("preprocessCore")
normalize.quantiles(datamatrix,copy=TRUE)