Question: Batch correction for TCGA 450K data
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gravatar for aditi.qamra
3.1 years ago by
aditi.qamra260
Toronto
aditi.qamra260 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!

 

tcga dna methylation 450k • 1.9k views
ADD COMMENTlink modified 23 months ago by Biostar ♦♦ 20 • written 3.1 years ago by aditi.qamra260

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

ADD REPLYlink written 3.1 years ago by Ying W3.9k
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