Fig. 2.

Technical reproducibility and biological variability. On the left, scatterplots of normalized peptide reactivity values of (A): 2 technical replicates assayed with sample A (Pearson's correlation coefficient, PCC = 0.93), and (B) two different biological samples (sera pools A and B, PCC = 0.54). On the right, normalized peptide reactivities were grouped by source protein to calculate protein-wise reactivities, as described under “Experimental Procedures.” In these scatterplots of protein reactivities, biological variability between sera pools at the level of proteins can be observed. In panel C, signals from 2 individual sera pools/chip assays were compared, whereas in panel D, signals from pairs of pools were averaged before plotting. Green points represent query proteins, black points the randomly generated sequences and blue points, antigens with previously validated epitopes. Vertical and horizontal lines, mark the cut-off, calculated as described under “Experimental Procedures.” Using this cut-off, Sample A and B share 44% of reactive proteins (panel C), and the averaged signal from the two sera pools (labeled A and C) share 70% of reactive proteins with the averaged signal from two other pools (labeled B and D, panel D).