Hi,

   I had samples with three groups,"Control","TreatA","TreatB".

For each gene, I used DESeq2 contrast to get the p-values of "TreatA vs Control" , "TreatB vs Control" and "TreatA vs TreatB".

   Now I want to test the hypothesis that: The expression of Gene X is not changed in any of these three groups (H0). Anyone knows how to get the p-value for this test?

  For our daily bio-experimental data, we could F-test.  For this RNAseq specific data, could I just use the smallest p-value among these three comparisons instead? 

Thanks very much!

Raymond

You can use a Likelihood Ratio Test. Take a look at the vignette section on this topic and the help pages for ?DESeq and ?results.