We all know that given a profiling of gene expression data and two, maybe more, groups or subtypes, we could derive differentially expressed genes between these groups.
However, how to determine this kind of differential mutations or SNPs between groups by any stat-of-the-art methods.
To my knowledge, the popularly used algorithms like MutSigCV, MutSiC, they determined the cancer drivers among all the samples with a specific cancer. I am not sure if I performed MutSigCV twice for two subtypes separately, and compared the results means anything correct.
Thus, does anyone have better ideas about this issue, i.e., how to find 'robust' differentially mutated genes, or driver mutations between subtypes by whole exome sequencing.
Many thanks advanced!