From: Identifying biological themes within lists of genes with EASE

Method | A | B | C | D | E | F | G | H | |||
---|---|---|---|---|---|---|---|---|---|---|---|

Normalization | MAS 4 | MAS 4 | dChip | dChip | Rank remap | Rank remap | NP | NP | |||

Intensity calculation | MAS 4 | MAS 4 | dChip | dChip | dChip | dChip | dChip | dChip | |||

Method | Normalization | Intensity calculation | Gene selection |
t-test
| SAM |
t-test
| SAM |
t-test
| SAM | t-test | SAM |

A | MAS 4 | MAS 4 |
t-test
| [72] | 72 (60%) | 20 (7%) | 17 (12%) | 18 (8%) | 19 (12%) | 24 (8%) | 22 (10%) |

B | MAS 4 | MAS 4 | SAM | [120] | 27 (9%) | 22 (12%) | 25 (9%) | 25 (13%) | 34 (10%) | 31 (12%) | |

C | dChip | dChip |
t-test
| [220] | 81 (36%) | 130 (48%) | 70 (27%) | 105 (29%) | 71 (22%) | ||

D | dChip | dChip | SAM | [86] | 56 (27%) | 55 (40%) | 49 (18%) | 47 (27%) | |||

E | Rank remap | dChip |
t-test
| [180] | 95 (50 %) | 109 (35%) | 76 (32%) | ||||

F | Rank remap | dChip | SAM | [105] | 68 (24%) | 67 (59%) | |||||

G | NP | dChip |
t-test
| [242] | 154 (59%) | ||||||

H | NP | dChip | SAM | [173] |