How does edgeR normalize sequencing depth
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6.8 years ago
hxlei613 ▴ 90

Hi everybody!

I just started to use edgeR.And I am curious about the normalization methods used to normalize sequencing depth. But I can't find exact methods in edgeR UsersGuide. It only mentions TMM method that can adjust RNA composition.

Is there someone to help me?

Thank you very much!

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6.8 years ago

TMM is described here.

Yes, it deals with sequencing depth in a robust way.

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I have read this already. But I want to figure out the methods used to normalize sequencing depth in edgeR. Thank you any way :)

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TMM is the method used to normalize for sequencing depth. In fact, it works better than simply correcting by library size (see Figure 2 in the paper).

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