I have 4 RNAseq samples, both at Day 0 and Day 3. So total 8 samples.
I want to do differential Expression analysis between Day 0 and Day 3,but pairwise.
I wanted to confirm if this is The best way to do this is using multi-factor design ? from DEseq2 package. The condition of interest should go at the end of the design formula, e.g. ~ subject + condition. Does my metadata look fine for multi-factor design ?
Sample Subject Condition Sample1_day0 Day0 Rep1 Sample2_day0 Day0 Rep2 Sample3_day0 Day0 Rep3 Sample4_day0 Day0 Rep4 Sample1_day3 Day3 Rep1 Sample2_day3 Day3 Rep2 Sample3_day3 Day3 Rep3 Sample4_day3 Day3 Rep4
Also, When we do differential expression of 1 group vs the other normally (without multicondition), we get results in the form of 1 log foldchange column ,1 p value column etc. How would we get the results in this ?