Dye effects: non spike-in probes. This figure shows the distribution of dye effects. The actual distributions are shown in blue and null distributions are shown in black. Pre-processing methods are compared across columns. In the top row moderated t-statistics are used to measure dye effect. The null distribution was obtained by randomly changing the sign of half of the log ratios for each gene before calculating the t-statistic. Gene specific dye effects are indicated by the heavy tails on the blue curves compared to the black curves of the null distribution. There is also a slight shift to the right for the Agilent processed data and the loess normalized, background subtracted data. In the bottom row, observed distributions of dye effects, as measured by the mean fold changes, are shown to give a sense of their scale. The relationship between null and observed distributions is similar to that seen with moderated t-statistics and is not shown here. Dye effects tend to be small regardless of the pre-processing method used.