Question

gene expression data analysis and batch effect methods

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tati6406 • 0

@tati6406-10823

Last seen 6.8 years ago

I have a gene expression data including intrinsic subtypes of breast cancer, but it does not have paired normal samples, Is it possible to use normal samples from different batch if I use batch effect removal methods eg COMBAT or DWD?

batch effect gene expression • 1.1k views

ADD COMMENT • link updated 7.5 years ago by chris86 ▴ 420 • written 7.5 years ago by tati6406 • 0

score 2 · Answer 1 · 2017-05-31

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chris86 ▴ 420

@chris86-8408

Last seen 4.9 years ago

UCL, United Kingdom

You cant remove batch effects if the data is 100% confounded.

Better just to ignore the normals.

ADD COMMENT • link 7.5 years ago chris86 ▴ 420