(A) Highly reproducible systematic errors from gene-dye interactions. The arrows demonstrate intense red dye labeling for a given gene spotted in duplicate both for the T/C slide where the treated sample is labeled with red dye (Cy5) and control sample is labeled with green dye (Cy3), as well as in the C/C slide where the same sample is labeled both red and green. (B) Experimental designs. Two different experimental methods were compared: A dye-swap approach, where the dye color is reversed for T/C hybridizations, and a "control correction" design, where T/C and C/C hybridizations are performed without reversing the dyes. T denotes the neuregulin treated cells, while C denotes the untreated, control cells. Each arrows represent a replicate and the tails of the arrows indicate cy5 labeling and the heads indicate cy3 labeling. (C) Data processing flow chart for the control correction method.