Figure 5
From: Microarray scanner calibration curves: characteristics and implications
Accuracy and underestimation of log ratios. The correlation of true log ratios (StLgR) versus log ratios estimated by fluorescence intensities under different combinations of Cy5/Cy3 PMT gain settings reveals systematic ratio bias. Intensity data are mean-zero normalized for each individual channel at each PMT gain. The log ratios are estimated from different Cy5/Cy3 PMT gain combinations; A: 400 V/400 V; B: 700 V/700 V; C: 900 V/900 V; D: 400 V/700 V; and E: 700 V/400 V. Figure 5E corresponds to a dye-swap pair in which the Cy5/Cy3 PMT gains are set to 400 V/700 V and 700 V/400 V for the X- and Y-axes, respectively.