Hi All, I've been trying to wrap my brain around DeSeq2's design model. I was given samples coming from : 2 cell lines, grown in 2 medias, with 2 different vectors. Is there a way to capture all of the interactions? For example:

Base differences between cell lines Base differences within cell line, between medias. Base differences within cell line, within medias, between vectors.

I've tried a couple of different strategies, but am getting a bit lossed in the complexity:

The first way was to group replicates into groups, meaning CellLineMediaVector design = ~Group

The second was trying something like: design = ~ CellLine + Media + Vector + Media:Vector + CellLine:Vector + CellLine:Media

The third being the LRT method design = ~ CellLine + Media + Vector + Media:Vector reduced = ~ CellLine + Media + Vector

Any tips or advice would be great, thanks

I’d recommend collaborating with a statistician to explore what type of statistical design to use to answer various questions. I don’t have time to provide extensive statistical consultation on this site but instead try to limit to software questions.