Question: Batch correction for TCGA 450K data
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aditi.qamra • 260 wrote:
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!
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modified 2.6 years ago
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Biostar ♦♦ 20
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written
3.8 years ago by
aditi.qamra • 260
I think you need to correct for batches, have a look [here](http://bioinformatics.mdanderson.org/main/TCGABatchEffects:Overview)