Table 1. Estimated bias for the three Brooks et al. (2015) mixture experiments.
The first three columns show the bias estimated in each mixture experiment; the second three columns show the bias estimated for individual protocol steps from the mixture estimates. In each case, bias is shown as relative to the average taxon; that is, the efficiency of each taxon is divided by the geometric mean efficiency of all seven taxa. The last three rows summarize the multiplicative error in taxon ratios due to bias and noise. Taxa are ordered by decreasing efficiency in the cell mixtures. Abbreviations: PCR prod.: PCR product; Seq. + Inf.: Sequencing + Informatics.
| Mixtures | Steps | |||||
|---|---|---|---|---|---|---|
| Taxon | Cells | DNA | PCR prod. | Extraction | PCR | Seq.+Inf. |
| Lactobacillus iners | 4.7 | 2.3 | 1.2 | 2.0 | 1.9 | 1.2 |
| Sneathia amnii | 4.6 | 2.4 | 1.3 | 1.9 | 1.8 | 1.3 |
| Lactobacillus crispatus | 2.3 | 0.5 | 0.9 | 4.3 | 0.6 | 0.9 |
| Prevotella bivia | 1.8 | 0.4 | 0.9 | 4.6 | 0.4 | 0.9 |
| Atopobium vaginae | 0.3 | 1.1 | 1.0 | 0.3 | 1.0 | 1.0 |
| Streptococcus agalactiae | 0.2 | 2.0 | 0.9 | 0.1 | 2.2 | 0.9 |
| Gardnerella vaginalis | 0.2 | 0.4 | 0.8 | 0.4 | 0.5 | 0.8 |
| Max pairwise bias | 29.3 | 6.1 | 1.6 | 36.6 | 5.2 | 1.6 |
| Avg. pairwise bias | 5.6 | 2.7 | 1.2 | 5.5 | 2.3 | 1.2 |
| Avg. pairwise noise | 1.2 | 1.2 | 1.3 | — | — | — |