DESeq2::lfcshrink() for complex contrast designs
1
0
Entering edit mode
@krutherford-15827
Last seen 5.9 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 • 1.3k views
ADD COMMENT
0
Entering edit mode
@mikelove
Last seen 1 hour 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.

ADD COMMENT

Login before adding your answer.

Traffic: 695 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6