Array and intensity-dependent variation can be corrected by normalization based on intensity. (A) This is an MA-plot before normalization for one of T/C slides that plots the log intensity ratios against the averaged intensities at both wavelengths: M = log (T/C) and A = 1/2log(T*C). The majority of the data is less than zero in a "banana" or "comma" shaped distribution. This demonstrates a systematic, intensity-dependent dye effect, prominent at lower intensities. (B) After normalization using the lowess function, the MA-plot shows a more even distribution at all intensities.