I am attempting to meaningfully compare two resulting list of significantly (padj < 0.05) differentially expressed genes in an experiment with a shared control, although I am getting unexpected results. This experiment used 5 replicates for each treatment and 5 shared controls.
For example, when comparing two different treatments against the control, this yields 1025 and 579 DE genes respectively. When comparing these two different treatments against each other, this only yields 18 DE genes. In addition, when looking at the shared genes of the resulting list when comparing the aforementioned two different treatments against the control, this yields 329 DE genes.
This is confusing, as it seems the two treatments are not that different from each other when directly comparing them against each other. But when comparing to the shared control independently, this tells a much different story. My question is - what may be the reason for this unexpected difference?
In addition, is there any available software or a better method to deal with these types of comparisons?