Hello

I have read the below post a couple of time throughly, I think by resolving my last ambiguity I will figure out my own problem

DESeq2 time series contrasts between timepoints

From the mentioned post, this part is not clear to me results(dds, contrast=list(c("time_4_vs_0", "conditionLD.time4")), test="Wald")

If we supposed SD as control, does this part say we are looking at the difference of LD compared to SD considering a dynamic of gene expression from 0 hour to 4 hours ?

Or, we are just looking at the impact of LD (ignoring comparison with control) from 0 hour to 4 hours?

Thanks for any help

It is the comparison of time 4 and time 0 for LD samples only. See the interactions diagram in the DESeq2 vignette, that may help.