No assumption of equal variance | Assume equal variance | No. of probe sets^{a} | |||||||
---|---|---|---|---|---|---|---|---|---|

FDR = 0.05 | FDR = 0.10 | FDR = 0.25 | FDR = 0.05 | FDR = 0.10 | FDR = 0.25 | % probe sets^{a} | B73 > Mo17 | Mo17 > B73 | |

B73 vs. Mo17 | |||||||||

11-day seedling | 1633 | 3284 | 7400 | 3135 | 4784 | 8726 | 9.3 | 767 | 866 |

Immature ear | 740 | 1732 | 4749 | 2031 | 3209 | 6269 | 4.1 | 442 | 298 |

19 DAP embryo | 3264 | 5355 | 8907 | 5108 | 6786 | 9935 | 18.4 | 1437 | 1827 |

B73 × Mo17 vs. Mo17 × B73 | |||||||||

11-day seedling | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |

Immature ear | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |

19 DAP embryo | 0 | 0 | 0 | 0 | 0 | 214 | 0 | 0 | 0 |

Analysis of differential expression in B73 relative to Mo17 or B73 × Mo17 relative to Mo17 × B73. Differentially expressed genes were identified using a one-way ANOVA to test GC-RMA values. Tests were performed with and without an assumption of equal variance with a Benjamini–Hochberg multiple testing correction and varying false discovery rates (FDRs).

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*a*These calculations are based on the list of differentially expressed genes identified using no assumption of equal variance and an FDR = 0.05.