( M(Arb), M(Opt))-Scatterplot analysis of BT-474_01 data This plot compares the calibrated ratios obtained by LOWESS (d = 1) with arbitrary (f
= 0.2) and optimized bandwidth windows for the first replicate hybridization of the BT-474 breast cancer cell line. Again, the line of unity slope shows where all the points should lay if both calibration methods produced identically calibrated ratios. Many points deviate from the similarity line in this example and such results are commonly observed for the microarray data used in this study. Consequently, it is clear that the choice of f
greatly affects how the data is calibrated. Points that are furthest away from the similarity line are highly influenced by the choice of f
in LOWESS calibration.