Hello,

I have been having some trouble wrapping my head around what is exactly being compared when you do a likelihood ratio test.

In RNA-seq workflow: gene-level exploratory analysis and differential expression when looking at the fission dataset it says that

library("fission")
data("fission")
ddsTC <- DESeqDataSet(fission, ~ strain + minute + strain:minute)
ddsTC <- DESeq(ddsTC, test="LRT", reduced = ~ strain + minute)
resTC <- results(ddsTC)

"Genes with small p values from this test are those which at one or more time points after time 0 showed a strain-specific effect."

My Question is if I set up the experiment as follows:

ddsTC <- DESeqDataSet(fission, ~ strain + minute)
ddsTC <- DESeq(ddsTC, test="LRT", reduced = ~ minute)
resTC <- results(ddsTC)

What would the small p-values be indicating in this design? My intuition is that this would find genes where there is a strain-specific effect over all the time points; would that be right?

Thanks a lot!

The LRT you set up above is testing if there are any differences due to strain. It assumes in the full model that the strains have the same profile over time, except allowing for shift at all time points due to strain differences. Because there is no interaction term, the strains cannot have different profiles over time.

We have a diagram of interaction terms in the vignette that might be useful for you.