Question: How to normalized the different cancers of Level 3 TCGA data of DNA Methylation
1
gravatar for sheny
4.4 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 • 2.0k views
ADD COMMENTlink modified 2.4 years ago by Biostar ♦♦ 20 • written 4.4 years ago by sheny20
1

Anybody knows how to normalize the beta distributed data. Thanks

ADD REPLYlink written 4.4 years ago by sheny20

Thanks so much. It is useful

ADD REPLYlink written 4.3 years ago by sheny20
2
gravatar for Shicheng Guo
4.4 years ago by
Shicheng Guo8.1k
Shicheng Guo8.1k wrote:

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

library("preprocessCore")
normalize.quantiles(datamatrix,copy=TRUE)
ADD COMMENTlink modified 3 months ago by RamRS26k • written 4.4 years ago by Shicheng Guo8.1k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1090 users visited in the last hour