TABLE 1

Identification of differentially expressed genes

No assumption of equal varianceAssume equal varianceNo. of probe setsa
FDR = 0.05FDR = 0.10FDR = 0.25FDR = 0.05FDR = 0.10FDR = 0.25% probe setsaB73 > Mo17Mo17 > B73
B73 vs. Mo17
    11-day seedling1633328474003135478487269.3767866
    Immature ear740173247492031320962694.1442298
    19 DAP embryo32645355890751086786993518.414371827
    B73 × Mo17 vs. Mo17 × B73
    11-day seedling000000000
    Immature ear000000000
    19 DAP embryo00000214000
  • 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).

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