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, Knock-down_3). So all together there are 36 samples from all 3 time points.
Now I want to compare every Knock-down sample within a particular time point to its Control samples within the particular time point.
So for this type of analysis,
a) Should I include all the 36 samples all together in the count matrix and later contrast to specify the sample vs samples in DESeq2
b) Should I include only samples within the particular time point(12 samples) in the count matrix and compare all Knock-down samples with respect to Control sample using DESeq2
c) Should I include only two samples within a time point in count matrix and compute diff. expressed genes using DESeq2
Thanks in advance