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Table 4 Accuracy, sensitivity, PPV and F-Score in % for the First 454 dataset and fold change threshold f of 1, 1.5, and 2.

From: Bootstrap-based differential gene expression analysis for RNA-Seq data with and without replicates

Fold Change Method Accuracy % Sensitivity % PPV % F-Score %
  FisherTotal 34.01% 30.50% 95.63% 46.24%
  FisherHousekeeping 24.52% 20.12% 94.74% 33.38%
1 GFOLD 55.62% 54.18% 92.11% 68.23%
  IsoDE-Match 75.33% 79.57% 77.41% 78.47%
  IsoDE-All 78.85% 84.67% 81.04% 82.82%
  FisherTotal 48.18% 35.37% 89.81% 50.75%
  FisherHousekeeping 42.48% 24.86% 97.74% 39.63%
1.5 GFOLD 62.19% 58.13% 85.39% 69.17%
  IsoDE-Match 64.09% 74.19% 72.52% 73.35%
  IsoDE-All 72.85% 79.54% 80.62% 80.08%
  FisherTotal 57.96% 39.53% 85.43% 54.05%
  FisherHousekeeping 55.33% 29.30% 97.67% 45.08%
2 GFOLD 69.05% 61.16% 83.49% 70.60%
  IsoDE-Match 67.15% 76.51% 70.30% 73.27%
  IsoDE-All 75.18% 80.93% 78.03% 79.45%
  1. The number of bootstrap samples is M = 200 for IsoDE-Match and M = 20 for IsoDE-All, and bootstrap support was determined using the binomial model with significance level α = 0.05.