Ratio of samples to do differential expression

Question

[Ron]

Hi all,

I have been doing differential expression for a while.One question that always comes to my mind is regarding the ratio of samples that can be compared between control vs treatment.

For e.g. Ideal scenario is to have equal number of controls and treatments. But sometimes when its not possible , and we have only 10 controls but 90 treatment samples.Is it ok to do such a comparison? Would there be any bias towards treatment samples?

Thanks

Ron