Figure 9.

Spatial effects of normalization on R/G ratios. One of the two cDNA arrays from the dye-swap study showing Cy5/Cy3 log-ratios with a yellow-cyan color scale and indications defining the print-tip sectors. Upregulated probes are shown in yellow, unchanged in black and downregulated in cyan. (a) log-ratios after global qspline normalization where spatial and/or print-tip effects can clearly be seen. (b) The array after scaled print-tip lowess normalization; a noticeable improvement over the global approach is shown, but spatial bias within print-tip sectors can still be seen. (c) After spatial normalization little if any spatial bias can be seen.