In non-nested experiments, biological replicates are independent. The following figure shows a study that investigates six different mice: three are untreated and three are treated. Each mouse has three different measurements. In this example, each mouse is a biological replicate, and the different measurements are technical replicates.
Non-nested longitudinal experiments are an extension of non-nested experiments. In these types of experiments, experimental groups are ordered, and you can test for temporal trends in the data. The following figure shows non-nested longitudinal biological and technical replicates.
In non-nested experiments, the application calculates abundances. After summing up sample abundances and normalization, it calculates abundances for the replicates as the median of the technical replicates, and then it calculates the sample group abundances as the median of the biological replicate abundances. It calculates ratios as the ratio of sample group abundances.
