Question: How to normalized the different cancers of Level 3 TCGA data of DNA Methylation
1
gravatar for sheny
3.5 years ago by
sheny20
United States
sheny20 wrote:

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? 

myposts • 1.7k views
ADD COMMENTlink modified 18 months ago by Biostar ♦♦ 20 • written 3.5 years ago by sheny20
1

Anybody knows how to normalize the beta distributed data. Thanks

ADD REPLYlink written 3.5 years ago by sheny20
2
gravatar for Shicheng Guo
3.5 years ago by
Shicheng Guo7.5k
Shicheng Guo7.5k wrote:

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

library("preprocessCore")

normalize.quantiles(datamatrix,copy=TRUE)
ADD COMMENTlink written 3.5 years ago by Shicheng Guo7.5k
0
gravatar for sheny
3.5 years ago by
sheny20
United States
sheny20 wrote:

Thanks so much. It is useful

ADD COMMENTlink written 3.5 years ago by sheny20
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