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Table 2 Accuracy, sensitivity, PPV and F-Score in % for MAQC Illumina 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 %

 

FishersTotal

70.41%

70.79%

91.24%

79.72%

 

FishersHousekeeping

65.60%

65.22%

95.05%

77.36%

1

GFOLD

78.13%

80.06%

92.67%

85.90%

 

Cuffdiff

11.37%

6.96%

100.00%

13.01%

 

edgeR

73.03%

73.26%

95.56%

82.94%

 

IsoDE-Match

82.63%

87.46%

83.70%

85.54%

 

IsoDE-All

82.22%

87.17%

82.82%

84.94%

 

FishersTotal

74.05%

78.20%

84.85%

81.39%

 

FishersHousekeeping

76.68%

73.61%

93.67%

82.44%

1.5

GFOLD

79.15%

79.35%

90.41%

84.52%

 

Cuffdiff

28.43%

8.60%

100.00%

15.85%

 

edgeR

80.01%

79.92%

92.07%

85.57%

 

IsoDE-Match

78.98%

86.23%

84.62%

85.42%

 

IsoDE-All

79.01%

86.42%

84.49%

85.44%

 

FishersTotal

78.43%

81.86%

82.44%

82.15%

 

FishersHousekeeping

81.20%

80.00%

88.21%

83.90%

2

GFOLD

82.94%

78.84%

92.37%

85.07%

 

Cuffdiff

40.96%

10.47%

100.00%

18.95%

 

edgeR

83.67%

81.63%

91.17%

86.13%

 

IsoDE-Match

82.04%

85.58%

85.19%

85.38%

 

IsoDE-All

81.20%

86.74%

83.07%

84.87%

  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.