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.
I have to say samples are not clustered very well on PCA plot...