Hello,

I'm working on a RNA-Seq study with the following design:

            1t - 1dpt        1t - 3 dpt       1 t - 5 dpt      2t - 1 dpt       2t - 3 dpt       2t - 3dpt
Control     3 replicates     3 replicates     3 replicates     3 replicates     3 replicates     3 replicates
Test        3 replicates     3 replicates     3 replicates     3 replicates     3 replicates     3 replicates

1t-1dpt: 1 treatment, RNA-Seq 1 day post-treatment

I want to determine if the number of treatments has an effect on gene expression for a list of genes of interest.

How should I proceed? I thought of taking the averages of the replicates in each cell and comparing them one to one (1t - 1dpt to 2t - 1dpt, etc.) with a paired t-test. I also want how this effect applied to genes in different metabolic pathways: I would use ANOVA. Is it right? Is there more analysis to be done?

Thanks!