Table 3.
Mutual predictability of the number of barley genes declared differentially expressed from seven data extraction methods.
| Methods | AD | MAS5.0 | MBEI1 | MBEI2 | RMA | PDNN | GCRMA |
| AD | 10066 | 5984(89%) | 7951(87%) | 8030(93%) | 7566(86%) | 9269(82%) | 6610(90%) |
| MAS5.0 | 5984(59%) | 6716 | 5257(57%) | 5289(61%) | 5614(64%) | 6243(55%) | 5067(69%) |
| MBEI1 | 7951(79%) | 5257(78%) | 9185 | 7674(89%) | 6969(79%) | 8206(72%) | 6048(83%) |
| MBEI2 | 8030(80%) | 5289(79%) | 7674(84%) | 8650 | 6744(76%) | 7830(69%) | 5946(81%) |
| RMA | 7566(75%) | 5614(84%) | 6969(76%) | 6744(78%) | 8824 | 8419(74%) | 6736(92%) |
| PDNN | 9269(92%) | 6243(93%) | 8206(89%) | 7830(91%) | 8419(91%) | 11339 | 6994(96%) |
| GCRMA | 6610(66%) | 5067(75%) | 6048(66%) | 5946(69%) | 6736(76%) | 6994(62%) | 7310 |
The diagonal cells show the number of genes declared from each method respectively at FDR = 0.01. The upper and lower triangles show the numbers and percentages (in parentheses) of the genes declared by method j (j = 1st,...,7th column) and also by method i (i = 1st,...,7th row, i≠j). For example, the 5984 genes in common to AD and MAS5.0 represent 89% of those detected by MAS5.0 but only 59% of those detected by AD.
1 MBEI PM only model
2 MBEI PM-MM model