Reproducibility of signal ratios and intensities. (A) Scatter plot showing the reproducibility between two biological repeats of an experiment where cells grown in minimal or rich media were directly compared to each other. The plot represents 4245 genes that gave measurable data in both experiments. The CV for the repeated experiment shown here is 5%. Just one gene shows an ~2-fold difference in ratios between the two experiments (just outside the outer lines). (B) Autocorrelation plot showing the distribution of Cy5 and Cy3 signal intensities from a single self-self experiment. Median signal intensities minus median local background intensities were determined and signals from replicate spots were averaged. Grey spots: data from 790 spots that were flagged 'absent' during analysis or initial data processing (see Methods). Blue spots: data from 4260 spots that were retained for evaluation. All the signal intensities from the blue spots are <2-fold different from each other (within outer lines).