Double normalising when using sva and deseq2
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BioinfGuru ▴ 30
@yagalbi-11519
Last seen 2 days ago
Ireland

Hi all,

I want to run sva and include the results in the design passed to deseq2 looking for degs.

Sva takes normailzed counts, but deseq2 takes raw counts and normalises also.

So if I proceed, the data will be normalise twice.

Is it ok to normalize twice?

Should I remove surrogate variables and de-normalize before passing to deseq2?

Should i run deseq2 but prevent it normalizing again?

I realise sva is not strictly necessary here, but I'm just using a simple example to identify the issue.

Regards, Kenneth

DESeq2 Normalisation Bulkrnaseq Svaseq • 106 views
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@mikelove
Last seen 13 hours ago
United States

We have an SVA and RUV example in the workflow.

Briefly it does not double normalize. The factors are estimated on scaled data and so DESeq2 will use these to remove variance after accounting for size factors through its own method.

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Thanks again Michael.

Found the work flow

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