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Table 1 Percentage of total genes with a significant p-value after each normalization technique. Site p-values correspond to the association of site with gene expression and Sample p-value corresponds to the association of sample and gene expression.

From: A protocol to evaluate RNA sequencing normalization methods

 

Raw

TMM

DESeq

Quant

RPKM

TPM

Log2

% site p-values<0.05

0.95

0.95

0.94

0.92

0.87

0.90

1.00

% sample p-values<0.05

0.37

0.27

0.35

0.34

0.36

0.49

0.69

Variance site p-values

1.40E-02

1.30E-02

1.39E-02

2.00E-02

2.73E-02

2.28E-02

4.44E-77

Variance sample p-values

8.73E-02

8.78E-02

8.61E-02

8.42E-02

8.62E-02

8.12E-02

6.37E-02

Median site p-value

2.28E-59

1.11E-64

5.22E-51

2.60E-58

1.64E-20

1.85E-35

0.00E+00

Median sample p-value

2.00E-01

2.98E-01

2.17E-01

2.30E-01

2.13E-01

5.71E-02

1.28E-05