Adding LRT test

Open wxicu opened this issue 2 years ago • 4 comments

Hey, thanks for developing pydeseq2! I used to perform DGE analysis with edgeR and happy now to see there is a python package. I am comparing the result of pydeseq2 and edger on the same dataset and I see there is a large difference. Is it possible to add likelihood ratio test like in deseq2 with dds = DESeq(dds, test="LRT") in the future? Thanks a lot!

Oct 04 '23 12:10 wxicu

Hi @wxicu, thanks for the suggestion! It's in our TODO list :) we hope to open a PR in the next few weeks

Oct 05 '23 08:10 BorisMuzellec

Hi, thanks for all your work with PyDESeq2. Any idea when the LRT changes are going to be pushed to production?

May 21 '24 00:05 bengroves

Hi @bengroves, unfortunately the LRT PR (#178) isn't currently being developed, but we'd be happy to help anyone who'd like to revive it or create a new one

May 21 '24 13:05 BorisMuzellec