DESeq2::lfcshrink() for complex contrast designs
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@krutherford-15827
Last seen 3.5 years ago

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! :)

deseq2 lfcshrink interaction term • 804 views
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@mikelove
Last seen 3 hours ago
United States

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.

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