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Table 1 Comparison between FPKM and SGTR methods according to transcript size

From: An integrative method to normalize RNA-Seq data

 

N

Samples

FPKM

log 2 (FPKM)

SGTR - Size

SGTR - Size and GC content

All genes

159

1475

1.07E-15

7.96E-39

1.71E-39

4.80E-39

Size < 1,000 bp

9

1475

9.59E-03

2.15E-02

1.58E-02

2.62E-02

1,000 – 2,000 bp

63

1475

1.86E-06

6.39E-18

4.71E-17

2.56E-17

2,000 – 3,000 bp

49

1475

2.81E-07

3.55E-14

1.75E-14

2.47E-14

3,000 – 4,000 bp

28

1475

3.25E-04

1.86E-06

1.86E-06

3.01E-06

Size > 4,000 bp

10

1475

1.56E-03

5.82E-03

6.95E-03

5.42E-03

All genes

155

1455

8.84E-16

2.95E-39

5.86E-39

3.40E-39

Size < 1,000 bp

9

1455

3.84E-02

1.03E-01

8.34E-02

1.05E-01

1,000 – 2,000 bp

60

1455

9.81E-07

1.57E-18

2.00E-17

4.19E-18

2,000 – 3,000 bp

50

1455

3.48E-09

9.07E-16

8.60E-16

1.43E-15

3,000 – 4,000 bp

26

1455

5.60E-05

2.80E-07

2.99E-07

4.50E-07

Size > 4,000 bp

10

1455

4.44E-03

2.26E-03

2.99E-03

1.96E-03

All genes

162

1479

4.63E-14

8.24E-44

1.37E-43

2.02E-49

Size < 1,000 bp

9

1479

7.54E-02

1.55E-01

1.18E-01

9.34E-02

1,000 – 2,000 bp

62

1479

1.75E-08

1.37E-16

6.87E-16

5.11E-18

2,000 – 3,000 bp

53

1479

1.68E-05

1.64E-19

1.64E-19

9.64E-22

3,000 – 4,000 bp

29

1479

1.67E-05

2.80E-09

3.08E-09

4.36E-10

Size > 4,000 bp

9

1479

1.33E-03

2.81E-05

5.39E-05

1.04E-04

All genes

152

1345

1.16E-14

1.57E-42

1.86E-42

6.11E-44

Size < 1,000 bp

9

1345

3.83E-02

9.84E-02

6.95E-02

7.98E-02

1,000 – 2,000 bp

58

1345

7.93E-08

6.39E-18

6.85E-17

2.43E-18

2,000 – 3,000 bp

50

1345

2.04E-05

8.39E-18

5.17E-18

1.74E-18

3,000 – 4,000 bp

26

1345

5.08E-03

7.67E-07

7.87E-07

1.01E-06

Size > 4,000 bp

9

1345

6.83E-04

1.62E-04

2.59E-04

4.44E-04

All genes

162

1476

2.73E-15

1.73E-41

6.74E-41

1.51E-44

Size < 1,000 bp

9

1476

5.12E-02

6.26E-02

4.52E-02

5.10E-02

1,000 – 2,000 bp

62

1476

3.38E-08

7.54E-17

4.72E-16

4.92E-18

2,000 – 3,000 bp

53

1476

1.55E-05

2.56E-17

3.53E-17

1.89E-18

3,000 – 4,000 bp

29

1476

3.44E-04

6.14E-07

7.13E-07

3.47E-07

Size > 4,000 bp

9

1476

9.18E-04

1.44E-04

2.76E-04

5.51E-04

  1. N corresponds to the number of analyzed genes. The five samples (1475, 1455, 1479, 1345, and 1476) refer respectively to samples with a total read number around 10.106, 13.106, 20.106, 24.106, and 30.106 reads. Abbreviations: SGTR size: correction for transcript size; and SGTR Size and GC content: correction for transcript size and GC content. Only the p-values of Pearson correlation with qRT-PCR quantifications are indicated. p-values were calculated using the Past3 program [24].
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BMC Bioinformatics

ISSN: 1471-2105

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