TABLE 2.
edgeR differential expression statistics
| Quantification method | Cluster | No. of correct DE genes | No. of correct NDE genes | No. of missed DE genes | No. of false-positive DE genes | Detection rate (%) | False-positive rate (%) | No. of DE genes excluded from expression threshold | No. of NDE genes excluded from expression threshold |
|---|---|---|---|---|---|---|---|---|---|
| Salmon –validateMappings –allowDovetail |
1 | 946 | 3,115 | 314 | 44 | 75.08 | 1.39 | 98 | 5 |
| Salmon –validateMappings |
1 | 946 | 3,115 | 314 | 44 | 75.08 | 1.39 | 98 | 5 |
| Kallisto | 1 | 947 | 3,116 | 313 | 43 | 75.16 | 1.36 | 141 | 4 |
| eXpress -B10 –no-bias-correct |
1 | 831 | 3,137 | 429 | 22 | 65.95 | 0.70 | 237 | 14 |
| eXpress | 1 | 53 | 3,143 | 1,207 | 16 | 4.21 | 0.51 | 292 | 17 |
| featureCounts | 2 | 936 | 3,135 | 324 | 24 | 74.29 | 0.76 | 169 | 15 |
| FADU –remove-multimapped |
2 | 974 | 3,127 | 286 | 32 | 77.30 | 1.01 | 153 | 15 |
| HTSeq -m intersection-nonempty |
2 | 903 | 3,128 | 357 | 31 | 71.67 | 0.98 | 267 | 17 |
| HTSeq -m union |
2 | 909 | 3,119 | 351 | 40 | 72.14 | 1.27 | 295 | 20 |
| HTSeq -m intersection-strict |
2 | 802 | 3,134 | 458 | 25 | 63.65 | 0.79 | 499 | 42 |
| HTSeq -m union –nonunique all |
3 | 1,006 | 3,113 | 254 | 46 | 79.84 | 1.46 | 76 | 6 |
| featureCounts -O | 3 | 1,008 | 3,116 | 252 | 43 | 80.00 | 1.36 | 80 | 6 |
| featureCounts -O –fraction |
3 | 1,000 | 3,112 | 260 | 47 | 79.37 | 1.49 | 109 | 6 |
| FADU –em_iterations 10 |
4 | 955 | 3,122 | 305 | 37 | 75.79 | 1.17 | 112 | 10 |
| FADU | 4 | 947 | 3,125 | 313 | 34 | 75.16 | 1.08 | 111 | 9 |