We are using limma to perform differential expression analysis among 3 different groups.
The problem (or not) is that the design is unbalanced. The sample size per group is very different (7, 9 and 39 samples). So, we decided to do a random selection from the big group to balance the design and to avoid different variances (assume homoscedasticity).
We don't know if it is better to balance the design or not (in terms of statistical power).
Thanks in advance :-)