If I understand correctly, TMM-normalisation has two assumptions: 1. Most genes are not DE 2. Comparable number of DE genes that are up/down-regulated (i.e. symmetry)
According to my analysis (I am using limma-voom workflow), one of my contrasts yield 200 DEGs, 90% of which were upregulated. Does it mean that the assumptions break?
My second question: is it a good practice to review the previous steps in DE analysis after taking a look at the results?
Best regards, Mikhael