I have a RNA seq data performed at different time points. So for every time I have 4 samples(Control, Knock-down_1, Knock-down_2, Knockdown_3) and I want to compare every Knock-down samples to its Control samples. As DESeq2 two set of samples to predict the Diff. expressed genes, how the analysis can be carried out:
a) Includes all samples from this particular time point and later use contrasts function to find the Diff expressed genes between specific samples OR b) Include only the two samples for which you want to find the Diff expressed genes and finish the analysis.
Thanks in advance