I have four groups, let's call them A, B, C, and D. I want to do all six comparisons:

1. A to B
2. A to C
3. A to D
4. B to C
5. B to D
6. C to D

but right now using my code I can only get the first three, with A always being compared to. How do I do this? My code is below.

# Assign conditions. I have three replicates in each group except for the fourth group I'm calling CD49a which has two replicates. (condition <- factor(c(rep("CD103", 3), rep("DP", 3), rep("DN",3), rep("CD49a",2))))

When I resultsNames the variable I'm storing my deseq() argument in, I only get things getting compared to A.

What should I do? Thanks in advance.

You can compare any subgroup to any subgroup using contrast in the results commend, instead of name.

ReusltsNames is behaving the way it is because you've let it set the reference level the default way. You can override this, and make the reference level whatever you want.