Figure 1

The relationship between absolute value, limit fold change (LFC), and variance across the absolute expression range. A) The various curves indicate the LFC required at different absolute values in order to be considered a significantly changed gene. As the selection criteria increases, the LFC increases, indicating that the 5% fold change model (green line) is more permissive than the 1% fold change model (red line). The various fold change models produced the curves with the following equations: A) in the liver: 5% LFC model = 1.52 + (100/absolute value); 3% LFC model = 1.55 + (140/absolute value); 1% LFC model = 1.70 + (185/absolute value). B) Examining the variance of each gene across the four dietary treatments enables the identification of those genes determined significantly changed. (•) represents genes below the 99.9% confidence level, () represents those genes selected by the 5% fold change model, and (+) represents those genes above the 99.9% confidence level. The various lines represent different confidence levels (i. 99.9%, ii. 99.999%, and iii. 99.99997%). As the fold change model increased (5% → 1%), concordance between the fold change model and the variance data (at a confidence level of 99.9%) increased (embedded table: x(y%), where x represents the number of genes with concordance (and y the percentage of genes with concordance)).