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Table 3 Comparison of preprocessing data sets by GC-RMA or MAS5 algorithms on the significance of fixed factors as revealed by LMMA analyses

From: Infection and genotype remodel the entire soybean transcriptome

FDR (TST)a Fixed factorb Number significant genesc Number matchesd Percentage matchese
   GC-RMA MAS5   
0.05 Genotype 27,156 26,651 25,896 97.2
  Treatment 27,732 27,585 27,099 98.2
  Genotype × Treatment 26,500 25,932 24,977 96.3
  Time 9,960 9,038 6,961 77
0.01 Genotype 25,923 25,162 24,024 95.5
  Treatment 27,139 26,864 26,079 97.1
  Genotype × Treatment 24,669 23,643 22,327 94.4
  Time 4,453 3,655 2,941 80.5
0.001 Genotype 24,191 23,161 21,780 94
  Treatment 26,351 25,962 24,873 95.8
  Genotype × Treatment 22,381 20,924 19,507 93.2
  Time 2,025 1,551 1,348 86.9
0.0001 Genotype 22,611 21,270 19,800 93.1
  Treatment 25,560 25,126 23,817 94.8
  Genotype × Treatment 20,293 18,691 17,256 92.3
  Time 1,173 857 768 89.6
  1. aFalse discovery rate (FDR) was controlled using the two-stage linear step-up method (TST). 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), and the genotype × treatment interaction. cNumber of significant genes for a factor was determined by LMMA analysis with FDR control. dThe number of genes called significant following GC-RMA and following MAS5 pre-processing. eThe number of matches as a percentage of the minimum of the number of significant genes called following GC-RMA or MAS5 preprocessing.