Figure 3

Effect of peptide efficiency factor. Various quantities plotted as a function of the lower bound of peptide efficiency factor (the upper bound is fixed at 1). (a) Mean quantification error as defined in Eq. (12). (b) Percentage of observed differentially expressed marker proteins at a 0.05 significance level. (c) Missing value rates at the protein and peptide levels. (d) Classification error rates given by LDA and KNN classifiers, respectively.