My experiment have several treatments (e.g. A, B, and C).
If I have interest in differentially expressed genes (DEGs) over all treatments, ANOVA will be good enough.
However, my major focus is identification of DEGs between two treatments, but came into trouble with adjusting p-values. What will be the best solution for adjusting p-values?
just perform multiple test correction (e.g. p.adjust function of R) using p-values from each pairwise comaprisons (e.g. A vs B)?
collect all p-values from all pairwise comparisons (A vs B, A vs C, B vs C) and run single multiple testing correction and report q-values?
any best solution for this?
Thank you in advance.