Figure 3

Average bias curves. Average bias curves (i.e. the loess smoothers) from MVA plots examining reproducibility in light of various systematic factors. The left set of six are pre-normalization; the right set of six are post-normalization. (A) Within plate technical replicates for the four cell lines on all four SAMs (n = 16 curves). (B) Within plate patient technical replicates for 200 ng of extraction 1 on first three SAMs (n = 15 curves). (C) Cell line technical replicates between SAMs (n = 24 curves). (D) Patient sample technical replicates between SAMs for 200 ng of extraction 1 (n = 15 curves). (E) Patient sample between extraction technical replicate for 200 ng (n = 5 curves). Replicate 1 was chosen arbitrarily. (F) Patient samples from extraction 1 comparing 25, 100, 400, 800 ng to 200 ng for two patients (n = 10 curves). Replicate 1 for 200 ng was chosen arbitrarily.