Entering edit mode
I have analysed the RNA-Seq mouse data knockout vs wildtype but the knockout genes that should be downregulated are showing upregulated and moreover the padj values are same for most of the genes that means padj values are equal for more tham half of the genes. Can anyone help me out in resolving this issue?
Without providing details, what you are saying is that you did some stuff and don't like what happened. When you posted this question, you had to delete some words to the effect of 'Post your code and the output you don't like right here'. Which you did not do, and without which nobody can possibly help you.