Say, I have RNa-seq data for three conditions: control and two mutants (4 biological replicates per each condition). Next, I perform Kallisto quantification and compare results via Sleuth LRT/WT tests in a pairwise manner (e.g. comparison between each mutant type and control and between two mutants). Since mutant conditions are mutually exclusive, two questions arise during these comparisons:
1) Is there any correction (apart from BH-adjusted p-value automatically calculated by Sleuth for each test) I have to use after all comparisons are done?
2) Among DEGs estimated by comparison of two mutant strains, more than half are genes found in comparisons between any (or both) of two mutants and control. Can I exclude them from results of between-mutant test?
Any links to external sources or publications would be of much help.
Looking forward to your comments!