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Table 2 Differences among sub-groups as revealed by LMMA analyses of data sets preprocessed by GC-RMA (TST-FDR)

From: Infection and genotype remodel the entire soybean transcriptome

FDRa Fixed factorsb 2 Sub-Groupsc 6 Sub-Groupsd
   Number significante Percentage significantf Number significante Percentage significantf
0.05 Genotype 26,043 91.9 25,975 91.6
  Treatment 27,191 95.9 27,180 95.9
  Time 4,748 16.7 4,735 16.7
  Genotype × Treatment 24,837 87.6 24,774 87.4
  Sub 45 0.2 235 0.8
  Sub × Genotype 458 1.6 238 0.8
  Sub × Treatment 251 0.9 429 1.5
  Sub × Genotype × Treatment 805 2.8 364 1.3
0.01 Genotype 24,808 87.5 24,732 87.2
  Treatment 26,652 94.0 26,645 94.0
  Time 2,692 9.5 2,692 9.5
  Genotype × Treatment 23,275 82.1 23,213 81.9
  Sub 0 0 20 0.1
  Sub × Genotype 68 0.2 42 0.1
  Sub × Treatment 35 0.1 74 0.3
  Sub × Genotype × Treatment 143 0.5 53 0.2
0.001 Genotype 23,268 82.1 23,150 81.7
  Treatment 25,891 91.3 25,881 91.3
  Time 1,468 5.2 1,465 5.2
  Genotype × Treatment 21,141 74.6 21,056 74.3
  Sub 0 0 0 0
  Sub × Genotype 4 0 3 0
  Sub × Treatment 5 0 9 0
  Sub × Genotype × Treatment 13 0 2 0
0.0001 Genotype 21,694 76.5 21,474 75.7
  Treatment 25,128 88.6 25,073 88.4
  Time 895 3.2 894 3.2
  Genotype × Treatment 19,265 68.0 19,131 67.5
  Sub 0 0 0 0
  Sub × Genotype 0 0 0 0
  Sub × Treatment 2 0 0 0
  Sub × Genotype × Treatment 1 0 0 0
0.00001 Genotype 20,105 71 19,845 70
  Treatment 24,310 86 24,264 86
  Time 585 2 583 2
  Genotype × Treatment 17,518 62 17,377 61
  Sub 0 0 0 0
  Sub × Genotype 0 0 0 0
  Sub × Treatment 0 0 0 0
  Sub × Genotype × Treatment 0 0 0 0
  1. aFalse discovery rate (FDR) was controlled the two-stage linear step-up method (TST-FDR). bThe fixed factors used in the LMMA model included genotype (V71-370, Sloan and VPRIL9), treatment (Upper, Lower, and Mock), time (9 am, 10:30 am, and 12 pm), sub (sub-group), and the interactions (genotype × treatment, sub × genotype, sub × treatment, and sub × genotype × treatment). c "2 Sub-Groups" refers to the 12 odd-numbered blocks compared to the 12 even-numbered blocks. d "6 Sub-Groups" refers to 6 randomly selected groups of blocks (four blocks in each group). eNumber of significant genes for a factor determined by LMMA analysis with FDR control. fThe number of significant genes as a percentage of the total number of detectable genes.