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!