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.
| 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 |