Table III. Average experimental thresholds as VSN ratio and -fold change that would encompass either 95 or 90% of naturally occurring technical variation for both same-same Erwinia data sets.
The average threshold was calculated for each data set as with four tags there are seven possible pairwise comparisons, and a 95% confidence interval is reported to give a measure of consistency. This analysis was completed where no filtering had occurred beyond the peptides being unique for a protein and the peptide being confident in its assignment to a protein.
| Percentile | Mean log ratio (VSN1−VSN2) | 95% confidence intervals for the mean log ratio |
Mean-fold change | 95% confidence intervals for mean -fold change |
||
|---|---|---|---|---|---|---|
| Lower | Upper | Lower | Upper | |||
| Erwinia B | ||||||
| 2.5 | −0.15 | −0.16 | −0.13 | 0.90 | 0.89 | 0.91 |
| 5 | −0.12 | −0.13 | −0.10 | 0.92 | 0.92 | 0.93 |
| 95 | 0.11 | 0.11 | 0.12 | 1.08 | 1.08 | 1.09 |
| 97.5 | 0.14 | 0.14 | 0.15 | 1.11 | 1.10 | 1.11 |
| Erwinia C | ||||||
| 2.5 | −0.12 | −0.13 | −0.11 | 0.92 | 0.91 | 0.93 |
| 5 | −0.09 | −0.10 | −0.09 | 0.94 | 0.93 | 0.94 |
| 95 | 0.09 | 0.09 | 0.09 | 1.06 | 1.06 | 1.06 |
| 97.5 | 0.11 | 0.11 | 0.12 | 1.08 | 1.08 | 1.09 |