Research Article
Differential Expression Analysis for RNA-Seq Data
Table 3
Comparison of methods on different datasets.
| Samples | Method | Number of genes present in only one samples | Number of genes present in both samples |
| Normal versus HL60 | likelihood ratio | 19 | 57 | Bayesian | 19 | 58 | DESeq | 0 | 3 | EdgeR | 0 | 4 |
| Normal versus K562 | likelihood ratio | 2 | 57 | Bayesian | 2 | 53 | DESeq | 0 | 3 | EdgeR | 0 | 1 |
| Globin reduced versus nonreduced | likelihood ratio | 7 | 2513 | Bayesian | 7 | 2344 | DESeq | 5 | 1505 | EdgeR | 7 | 2987 |
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