Hi, I am looking for genes with an interaction between a treatment and control group over four time periods. After performing a likelihood ratio test to determine whether this occurs at one or more time points, I have a set of genes meeting my cutoff for significance along with their associated log2 fold changes. My question is what do the log2 fold changes represent in a 2 x 4 interaction? I understand from a previous post (https://support.bioconductor.org/p/60543/) that I can think of the log2 fold change in a 2 x 2 interaction as a ratio of ratios, and this makes sense to me, but I am not sure how to extend that to a 2 x 4 interaction.

My design is

~ group + time + group:time

My likelihood ratio test is

DESeq(ddsHTSeqFILTERED, test="LRT", reduced = ~ group + time)

Thank you for any help you can give me in understanding this.

The interpretation of the interaction is the same in a 2x2 or 2x4 interaction model. It's the additional LFC compared the LFC at baseline (see also the diagram in the Interaction section of the vignette).