I have 3 groups of accepted hits, each group has 3 replicates. When I add 3 groups with corresponding replicates, the cuffdiff output only gave 2 groups comparison of differential expression, Please help me here
Cuffdiff does only pairwise differential expression testing, so each DE test will consider two groups, not three or more. However, Cuffdiff does iterate through and provide data for all possible group pairings. E.g.
A vs B A vs C B vs C