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Figure 1 | BMC Bioinformatics

Figure 1

From: The limit fold change model: A practical approach for selecting differentially expressed genes from microarray data

Figure 1

The relationship between absolute value, limit fold change (LFC), and variance across the absolute expression range. A) The x-axis threshold indicates those genes that have a minimum ADI of 20. Genes in bins of 200 are examined for the top 5% highest fold changes (red horizontal lines indicate the 95th percentile for each bin). The line of best fit, drawn through each bin in blue, identifies the overall LFC cut-off and is described by the simple equation 5% LFC = 1.74 + 91.55/min ADI. B) Identifying the top 1% (black line) or 10% (red line) highest fold changes in each bin shifts the LFC curve, when compared to the 5% LFC model (blue line), and alters the severity for the selection of differentially expressed genes (1% LFC = 2.43 + 166.12/min ADI; 10% LFC = 1.59 + 69.47/min ADI). C) The upper 99.9% confidence limit (CL) of a robust estimation of the coefficient of variance (CV) for replicates (within-treatment variability) has been modeled as a function of absolute minimum expression of all treatments, as indicated by the blue line. Overlaying the 99.9% CL on the data selected by the 5% LFC model (red dots) ensures high confidence in the selected genes.

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