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.

PercentileMean log ratio (VSN1−VSN2)95% confidence intervals for the mean log ratioMean-fold change95% confidence intervals for mean -fold change
LowerUpperLowerUpper
Erwinia B
    2.5−0.15−0.16−0.130.900.890.91
    5−0.12−0.13−0.100.920.920.93
    950.110.110.121.081.081.09
    97.50.140.140.151.111.101.11
Erwinia C
    2.5−0.12−0.13−0.110.920.910.93
    5−0.09−0.10−0.090.940.930.94
    950.090.090.091.061.061.06
    97.50.110.110.121.081.081.09