Table 1

Comparison of methods for identifying changes in gene expression

ParameterNumber falsely significantNumber called significantFDR
SAM
 Δ = 0.4134.928847%
 Δ = 0.578.119241%
 Δ = 0.656.116235%
 Δ = 0.919.18024%
 Δ = 1.28.44618%
 Δ = 1.2; R = 1.54.53412%
Fold change
 R = 2.0283.134881%
 R = 2.5137.816982%
 R = 3.076.89978%
 R = 3.546.76473%
 R = 4.029.33584%
Pairwise fold change
 R = 1.2245.635569%
 R = 1.3155.422071%
 R = 1.576.211865%
 R = 1.744.87064%
 R = 2.022.83860%
  • To increase the stringency for calling significant changes in gene expression, parameters for each method (Δ and R) were increased, as described in the text. The false discovery rate (FDR) was defined as the percentage of falsely significant genes compared to the genes called significant.