I am analyzing 20 Agilent microarrays from humans (20 subjects, two conditions) and yet there is no differentially expressed gene after adjusting for multiple testing (BH). I used Limma in R, tried different background correction as well as normalization methods (within and between arrays), I also tried to remove the least expressed probes to try to boost the signal. All the array quality checks looked fine.
The question is, if there are no significantly differentially expressed genes, what can be done? Has anyone ever tried to get some results out of this situation or has a good paper/link to suggest?