Question: Request for offset slot in DESeqDataSet objects
0
gravatar for jeroen.gilis
14 days ago by
jeroen.gilis0 wrote:

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.

edaseq deseq2 • 50 views
ADD COMMENTlink modified 14 days ago by Michael Love24k • written 14 days ago by jeroen.gilis0
Answer: Request for offset slot in DESeqDataSet objects
0
gravatar for Michael Love
14 days ago by
Michael Love24k
United States
Michael Love24k wrote:

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.

ADD COMMENTlink written 14 days ago by Michael Love24k
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