Figure 3.

2D-M plot for gel 4 and 12. Spatial gel plots for gel 4 and 12 (A) before, and (B-E) after normalization using different methods. A reconstructed gel image with increasing isoelectric point (pI) (left-right) and decreasing protein mass (top-down). For method A, B, E, F and G the M-values are calculated as log₂Cy5/Cy3 and for method C and D the M-values are calculated as log₂(Cy5/Cy2)/(Cy3/Cy2). The ten percent highest and lowest M-values in each gel are color coded red and blue respectively. For several of the normalization methods the spatial bias remains.