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
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