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 ?