Remove batch effect for many RNA-seq
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3.0 years ago
Shaway • 0

Hello every,

I a new comer for RNA-seq, here I have some questions for RNA-seq analysis.

I want to analyze about 10 type immune cells (more than 100 samples) and find the differential expressed genes. Now, I know that these data are from 12 different paper, I treat this as 12 batch then want to remove batch effect cause by different experiment.

Is it right for my understanding about batch effect?

Or I can do DE analysis just using TPM generated from raw counts.

Thank you, everyone!!

RNA-Seq batch effect ComBat sva • 1.3k views
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Entering edit mode
3.0 years ago
Ram 36k

You should model the batch as a covariate in differential expression analysis. Avoid ComBat if you can, I don't think "removing" batch effect is all that effective. IMO.

You could also use ComBat on TPM, but be careful in interpreting the results.

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Thanks for your help!

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