I have a complex RNA-seq experimental design like this :
condition subject A 1 A 2 A 3 A 4 B 1 B 2 B 3 C 5 C 6 C 7 C 8
First my goal is to compare A vs C condition but I also want to compare A vs B, which have some paired samples.
In my case it seems that
design=model.matrix(~subject+condition) will not work because my matrix is not of full rank.
Would you have any advice on how should I proceed to perform these 2 separate comparisons with paired and non-paired samples? Thanks in advance for enlightening me