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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].