I am using TCGA data in order to find differentially expressed genes. The cohort I am using has just 41 normal samples, while the tumor subtypes I am working with have measurements ranging from 80 to 140 samples. Is EdgeR (or any other equivalent package) an option or I cannot get significant results from this kind of analysis? I know that group sizes are not required to be the same in EdgeR, but is a comparison between 41 and 141 samples reliable?
Thank you in advance.