Hello, DESeq2 users,

I recently worked on differential expression analysis for a dataset containing 3 different treatments (A, B, and C). I called about 600 DE genes between group A and group C, 1 DE gene between A and B, and 0 DE gene between B and C.

I really would like to get some help about data interpretation here. Since groups A and B were so similar and A and C were different in about 600 genes, I expected that at least some hundreds of DE would be called between groups B and C. How do I get 0 between B and C here?

Thank you so much for your help.

C.

This can happen for many reasons and doesn’t indicate any issue with how you’ve run the code. You may want to look at a PCA plot to get a sense of the samples.