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Table 2 Median percent error (MPE) and 15% error fraction (EF.15) for isoform expression levels inferred from 30 M reads of length 25 simulated assuming geometric isoform expression.

From: Estimation of alternative splicing isoform frequencies from RNA-Seq data

Expression range

0

(0, 10-6]

(10-6, 10-5]

(10-5, 10-4]

(10-4, 10-3]

(10-3, 10-2]

All

# isoforms

13,290

10,024

23,882

18,359

1,182

66

66,803

 

Uniq

0.0

100.0

98.4

97.1

98.5

96.6

95.4

 

Rescue

0.0

294.7

75.5

49.2

30.4

28.3

71.9

MPE

UniqLN

0.0

100.0

80.8

30.3

26.4

24.8

36.0

 

Cufflinks

0.0

100.0

49.7

25.5

27.2

44.6

34.1

 

RSEM

0.0

100.0

31.9

13.5

11.4

13.0

21.2

 

IsoEM

0.0

100.0

25.3

7.3

3.2

2.2

12.0

 

Uniq

0.2

98.4

97.2

96.9

97.0

95.5

78.0

 

Rescue

48.4

95.5

86.2

73.1

61.5

56.1

76.0

EF.15

UniqLN

0.2

97.2

86.2

82.8

83.3

77.3

69.8

 

Cufflinks

17.6

96.4

81.3

71.0

74.7

80.3

67.9

 

RSEM

19.9

93.7

71.1

46.4

39.8

47.0

56.9

 

IsoEM

3.4

93.1

65.1

29.1

11.1

7.6

46.1