How to normalized the different cancers of Level 3 TCGA data of DNA Methylation
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?
1 answer
Actually, you can use quantile normalization to deal with this problem.
library("preprocessCore")
normalize.quantiles(datamatrix,copy=TRUE)
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Anybody knows how to normalize the beta distributed data. Thanks
Thanks so much. It is useful