I have an odd experimental design in that I have 4 conditions A, B, C, and D (all with replicates). However there is no "control" condition to compare to.
What I'm interested in is what genes are enriched in B compared to A, C, & D...ect. Is the best way to do this just using the "contrast" argument from results and doing all the comparisons pairwise, and then looking at the overlap of significant results? I'm a bit stumped as there is no reference condition.
What I'm interested in is what genes are enriched in B compared to A, C, & D...ect. Is the best way to do this just using the "contrast" argument from results and doing all the comparisons pairwise, and then looking at the overlap of significant results? I'm a bit stumped as there is no reference condition.
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