Hi I would to use DESeq2 to analyse NanoString miRNA expression data. I have a group of 5 - 6 conditioned group, and large set of controls available for comparison (>96). In this case I'm looking at different expression between two cancer types. If I include all cases in one analysis, how reliable would the results be? I also think about  breaking the controls into groups of 5-6 cases and perform multiple analysis to have equal size of conditioned and control groups. Would this work? Thanks!

This question was asked very recently on the site, but it’s hard to find similar questions. My answer was that it’s not technically a problem although the more samples in the small group the better obviously.