Table 1.
The number of DP genes called by the PSG test, FDM, Cuffdiff and combinations of the methods on pairs of samples from three sets: (A) HapMap, (B) Drosophila modENCODE and (C) ENCODE
| Sample 1 | Sample 2 | PSG | FDM | Cuffdiff | PSG  FDM |
PSG  Cuffdiff |
FDM  Cuffdiff |
All |
|---|---|---|---|---|---|---|---|---|
| (A) | ||||||||
| CEU Rep 1 | CEU Rep 2 | 0 | 0 | 1187 | 0 | 0 | 0 | 0 |
| CEU Rep 1 | Yoruban Rep 1 | 39 | 24 | 269 | 2 | 8 | 3 | 1 |
| CEU Rep 1 | Yoruban Rep 2 | 46 | 24 | 282 | 3 | 5 | 3 | 1 |
| CEU Rep 2 | Yoruban Rep 1 | 45 | 22 | 253 | 4 | 5 | 1 | 1 |
| CEU Rep 2 | Yoruban Rep 2 | 38 | 29 | 260 | 2 | 4 | 4 | 1 |
| Yoruban Rep 1 | Yoruban Rep 2 | 0 | 0 | 1253 | 0 | 0 | 0 | 0 |
| (B) | ||||||||
| CME_W1_Cl.8+ Rep 1 | CME_W1_Cl.8+ Rep 2 | 16 | 32 | 204 | 1 | 0 | 2 | 0 |
| CME_W1_Cl.8+ Rep 1 | Kc167 | 365 | 207 | 7 | 75 | 2 | 0 | 0 |
| CME_W1_Cl.8+ Rep 1 | ML-DmBG3-c2 | 232 | 164 | 6 | 46 | 1 | 1 | 0 |
| CME_W1_Cl.8+ Rep 1 | S2-DRSC | 406 | 228 | 12 | 86 | 6 | 1 | 1 |
| CME_W1_Cl.8+ Rep 2 | Kc167 | 319 | 211 | 16 | 72 | 4 | 3 | 1 |
| CME_W1_Cl.8+ Rep 2 | ML-DmBG3-c2 | 260 | 126 | 16 | 37 | 2 | 1 | 1 |
| CME_W1_Cl.8+ Rep 2 | S2-DRSC | 353 | 220 | 17 | 71 | 5 | 1 | 1 |
| Kc167 | ML-DmBG3-c2 | 384 | 321 | 12 | 93 | 2 | 1 | 1 |
| Kc167 | S2-DRSC | 419 | 209 | 12 | 88 | 6 | 2 | 1 |
| ML-DmBG3-c2 | S2-DRSC | 431 | 287 | 4 | 110 | 3 | 1 | 1 |
| (C) | ||||||||
| HUVEC Rep 1 | HUVEC Rep 2 | 35 | 43 | 440 | 6 | 2 | 4 | 1 |
| HUVEC Rep 1 | K562 Rep 1 | 376 | 344 | 8 | 113 | 2 | 0 | 0 |
| HUVEC Rep 1 | K562 Rep 2 | 379 | 302 | 12 | 81 | 6 | 2 | 2 |
| HUVEC Rep 2 | K562 Rep 1 | 442 | 382 | 8 | 144 | 4 | 3 | 3 |
| HUVEC Rep 2 | K562 Rep 2 | 355 | 285 | 10 | 80 | 3 | 2 | 2 |
| K562 Rep 1 | K562 Rep 2 | 224 | 308 | 168 | 39 | 8 | 8 | 1 |
Note: Pairs of samples that are technical or biological replicates are indicated in bold.