Figure 7

Median log-ratios by signal-based quartiles. Plots showing the median log-ratios (y axis) by quartiles (x axis) for each channel or array of experiments (rows) and for the different normalization methods (columns). The top row shows medians for the six arrays of the HIV experiment (control in green, HIV-infected in red) for data before normalization, after log-intensity scaling, lowess, rank-invariant set and qspline, respectively. The middle row shows medians for the 12 channels of the six glnA arrays (Cy3 in green and Cy5 in red) for data before normalization, log-intensity scaled by print-tip, scaled print-tip lowess, scaled print-tip qspline, and spatially scaled and smoothed (from left to right), respectively. The bottom row shows the four channels of the A. thaliana dye-swap replicate arrays 'A' and 'B', with wild-type channels in lower case, mutant in upper case, and with the same normalizations from left to right as were used in glnA plots above.