Type of Normalization done to TCGA level 3 Methylation Data

Question

[danhmed]

Hello! I have TCGA level 3 methylation data on CHOL and I want to replicate DMR analysis procedure in a paper I am reading but using different data than was used. Now, I know from TCGAs website that level 3 data is already normalized however, I not found any paper, or information on their site as to how normalization was done or at least what type of normalization was done.

I have two questions:

1. Can anyone point me to a resource that documents the specific normalization done on TCGA's level 3 methylation data?
2. Without knowledge on the normalization done, how much of an effect will the BMIQ normalization procedure have if I should use it before proceeding with my analysis?

Thank you.

Answer 1

[Zhenyu Zhang]

Which particular TCGA data you are talking about? the one on GDC with SeSAMe workflow? There is a SeSAMe paper. The hold hg19 annotated TCGA methylation data were processed by an older script from the same lab that developed SeSAMe.