Normalisation in DESeq2
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Bine • 0
@bine-23912
Last seen 10 hours ago

Dear all,

I need to describe in more detail how the built-in transformation of data of the DESeq2 function normalises raw counts. Can anyone give me a reference to a paper where this has been described? I have not been able to find anything yet, unfortunately.

Thank you so much, Bine

DESeq2 • 125 views
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ATpoint • 470
@atpoint-13662
Last seen 2 hours ago
Germany

If you have questions like that (how does tool x does y), the first step is always to read the paper a tool is based on. That in this case would be Love et al 2014. Searching for "normalization" will get you to the respective paragraph where they reference the original DESeq paper (Anders & Huber 2010) which describes the process in detail. Maybe easier to digest would be the StatQuest video breaking down the process nicely:

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Thank you very much, the video is great! I am trying to find the parts in the papers where I could reference to but cant see it. Are you referring to this paper: Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2 Michael I Love, Wolfgang Huber and Simon Anders 2014?

Thanks so much!

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Yes, this is also heavily cited throughout the manual/vignette.

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