Figure 4

Null distribution of fold-changes among all replicates. We calculated pair-wise fold-changes among five signal replicates (a total of 10 comparisons) for 12 650 probe sets (Chip U95A only) in three paradigms, for a total 378 750 fold-changes. Each point in the graph represents an observed fold-change and mean signal intensity for two identical samples of mRNA. The inset depicts all data points, magnified in the main figure to demonstrate that higher fold-change values are found at lower expression levels, even when the underlying expression is unchanged. This supports the notion that statistical significance of a fold-change depends on signal intensity.