Volcano plots. The negative log10-transformed p-values of the F1 test (see Box 3b) are plotted against (a) the log ratios (log2 fold change) in a two-sample experiment or (b) the standard deviations of the variety-by-gene VG values (see Box 3a) in a four-sample experiment. The horizontal bars in each plot represent the nominal significant level 0.001 for the F1 test under the assumption that each gene has a unique variance. The vertical bars represent the one-step family-wise corrected significance level 0.01 for the F3 test (see Box 3b) under the assumption of constant variance across all genes. Black points represent the significant genes selected by the F2 test with a compromise of these two variance assumptions.
Cui and Churchill Genome Biology 2003 4:210 doi:10.1186/gb-2003-4-4-210