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Question: DESeq2::lfcshrink() for complex contrast designs
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gravatar for krutherford
5 months ago by
krutherford0 wrote:

Hi there, I noticed that the lfcshrink() function in DESeq2 doesn't seem to work with more complex contrast designs, eg: those with interaction terms. Is it possible for this to be implemented? Thanks! :)

ADD COMMENTlink modified 5 months ago by Michael Love19k • written 5 months ago by krutherford0
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gravatar for Michael Love
5 months ago by
Michael Love19k
United States
Michael Love19k wrote:

This is implemented in the latest release:

https://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html#extended-section-on-shrinkage-estimators

You can use type="apeglm" or type="ashr" with designs with interaction terms.

ADD COMMENTlink written 5 months ago by Michael Love19k
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