Normalizing For Batch Effect In RNA-Seq Data
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7.6 years ago
Tom A ▴ 110

Hello,

Does anyone have a suggestion for dealing with "batch effect" between two batches of small RNA-Seq data? I've heard "ComBat" was good. Anyone have any others in mind?

Thanks in advance.

RNA-Seq combat principle-component batch-effect • 5.6k views
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This paper is worth a look. They tried several methods on array data (including "small" sample sizes), and concluded ComBat performed best: http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0017238

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7.6 years ago
Ann ★ 2.3k

The EdgeR package in Bioconductor can help with this. See the Arabidopsis data set in the User's Guide where samples were collected at different times.

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Thank you. I will give it a look over.

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6.0 years ago
tonja.r ▴ 500

Try RUVseq, they have three different approaches how to deal with batch effects based on empirical genes, in-spike genes and samples contrast. Also, take a look on PEER.

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6.0 years ago
Ron ★ 1.1k

I used combat and it does it pretty well.

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