Request for offset slot in DESeqDataSet objects
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@jeroengilis-21551
Last seen 3 months ago
Belgium

Hi all,

I am currently exploring normalization strategies such as EDASeq [ref; https://doi.org/10.1186/1471-2105-12-480] to address technical artifacts like GC-content and to account for both within­- and between-­lane normalization.

As illustrated in the EDASeq vignette, such normalization factors can be readily incorporated into the edgeR framework through the "offset" slot. This functionally is however not yet implemented in DESeq2.

Might it be possible to add this functionality? Any thoughts on this?

Kind regards,

j.g.

deseq2 EDASeq • 267 views
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@mikelove
Last seen 16 hours ago
United States

We have code in the DESeq2 vignette for how to incorporate EDASeq and cqn offsets, take a look there first. The DESeq2 normalization factors are a count scale offset — same thing but exponentiated.

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