How to compare specific genes between comparisons in RNA seq data

Question

[Omurice]

I have done differential gene expression analysis on a few comparisons for RNA seq. I am trying to narrow down my global analyses and select for specific genes and determine if they are differentially regulated between comparisons. Are there standards or statistical tools that I should use to determine if there is a difference (or not) in expression between comparisons (ex/ a gene upregulated in (1 vs 2) vs ( 3 vs 4)).

[seidel]

There's a section in the edgeR user manual called "Defining each treatment combination as a group" that examines nested interactions and looking at interactions between comparisons. It resembles the notation you have above, and can find genes behaving differently between your first and second comparisons.