In nested experiments, biological replicates are dependent; they might or might not be ordered. The different sample groups might represent the same individual under different conditions. In this case, you can have three different individuals, such as mouse 1, 2, and 3, under two different conditions, Untreated and Treatment 1.
In nested experiments, the application calculates abundances for biological replicates and sample groups as it does for non-nested designs, but it calculates the ratios differently. First, it calculates the ratios for biological replicates as a ratio of their abundances, and then it calculates sample group ratios as the median of the replicate ratios.
