Research Article
Differential Expression Analysis for RNA-Seq Data
Table 2
Assessing variability across replicates before and after normalization using the likelihood ratio method on 17708 genes.
| | Type of normalization | Percentage (number) of genes with similar count at different levels | | 1% | 2.5% | 5% | 10% |
| | No normalization | 97.6 (17294) | 95.7 (16956) | 93.1 (16501) | 87.5 (15496) | | TMM | 99.0 (17540) | 97.5 (17272) | 95.3 (16887) | 90.3 (16007) | | Quantile | 99.0 (17540) | 97.6 (17291) | 95.2 (16870) | 90.3 (16002) | | TPM | 86.50 (15318) | 86.31 (15284) | 85.90 (15212) | 84.50 (14964) |
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