|  | Abbr. | Description | Notes |
---|---|---|---|---|
Experimental choices | Number of replicates | NR | Number of technical or non-technical replicates for the two groups compared in the test | For simplicity, in many cases, we assume NR to be the same in both groups |
Number of data-points | ND | Number of data-points generated in the counting experiment | For example, reads generated in an RNA-seq experiment | |
Experimental characteristics | Entity count | EC | Number of entities in the counting experiment | For example, number of genes in an RNA-seq experiment |
Sample variability | SV | Variability across replicates (see Methods) | For example, biological variability in RNA-seq datasets | |
Abundance profile | AP | Relative abundance of the entities in the first group | Typically follows a power-law distribution | |
Perturbation profile | PDA, FC | Perturbations to the abundance profile of the first group to obtain the profile for the second group (see Methods) | Used to generate the differentially abundant entities (PDA = Percentage of entities, FC = fold-change distribution) | |
Test settings | Biases in data generation | Â | Deviations from multinomial sampling due to biases inherent in the experimental protocol | These are often corrected for in a preprocessing step, for example, composition bias in RNA-seq data [23],[24] |
Differential abundance test | DAT | See Table 2 |  |