Hi Dears

I am not very familiar with limma, I want use limma for finding DEGs of two different phenotype 

But there are some ambiguous issues for me in using limma for this work. Sample size of my phenotypes are completely different about 100 for control and 800 for case,now I don't know does limma could be use for this work that have big and unbalanced sample size?

There are no problems with using limma for unbalanced data sets.