Batch correction for TCGA 450K data

Question

[aditi.qamra]

Hi,

When working with Level 3 450K DNA methylation from TCGA, is there a batch correction and/or normalisation that is required?

1. While downloading the samples from https://tcga-data.nci.nih.gov/tcga/dataAccessMatrix.htm, the samples are listed in batch on applying filters. However I can't find the correct column to identify this batch information in the metadata sheets. Do we need to correct for this?
2. Does the level 3 data need normalisation across samples?

Thanks!

[Ying W]

I think you need to correct for batches, have a look [here](http://bioinformatics.mdanderson.org/main/TCGABatchEffects:Overview)