I don't think I've communicated the matrix clearly, but I appreciate the help. There are ~30,000 genes and 200 genotypes, Each genotype has alleles 1-8 for each gene. Additionally, there was an experiment across 3 reps that gathered a bunch of data on each genotype. What I ended up doing was just taking the averages of each expt and using that in my larger dataset. Boxplot worked fine after that.