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Table 4 Comparison of significant infection responses identified with SAS Proc Mixed LMMA or the non-parametric Wilcoxon signed rank test.

From: Infection and genotype remodel the entire soybean transcriptome

Data Pre-Processinga Genotype Infection Responseb Wilcoxonc LMMAd Number Matchesg Percentage matchesh
    Significante % sigf Significant % sig   
GC-RMA V71-370 Upper vs. Mock 23,016 81.2 20,418 72.0 20,406 99.94
   Lower vs. Mock 23,739 83.7 21,772 76.8 21,749 99.89
  Sloan Upper vs. Mock 24,369 86 22,758 80.3 22,712 99.8
   Lower vs. Mock 24,872 87.7 23,556 83.1 23,513 99.82
  VPRIL9 Upper vs. Mock 24,851 87.7 23,543 83.0 23,482 99.74
   Lower vs. Mock 25,260 89.1 24,180 85.3 24,087 99.62
MAS5 V71-370 Upper vs. Mock 22,300 78.7 19,486 68.7 19,478 99.96
   Lower vs. Mock 23,406 82.6 21,772 74.8 21,189 99.96
  Sloan Upper vs. Mock 23,984 84.6 22,758 78.5 22,208 99.82
   Lower vs. Mock 24,578 86.7 23,556 81.7 23,153 99.94
  VPRIL9 Upper vs. Mock 24,714 87.2 23,543 82.5 23,366 99.91
   Lower vs. Mock 25,144 88.7 24,180 85.4 24,165 99.81
  1. aThe data used for the analyses were either preprocessed using GC-RMA or using MAS5 algorithm as described in the Methods. bInfection responses relative to mock-inoculated tissue were evaluated for the upper infection court (Upper vs. Mock) and the lower infection court (Lower vs. Mock). cWilcoxon signed ranks test implemented by the wilcox.test function of R package stats version 2.6.0. dLinear mixed model analysis performed in SAS Proc Mixed. Model: y = Genotype + Treatment + Time + Genotype × Treatment + Block + Block × Genotype + Block × Treatment + Block × Time + Block × Genotype × Treatment + Error, where y refers to the log2 scale median polish summarized gene expression values, the main factors (Genotype, Treatment and Time) and the interaction Genotype × Treatment were fixed factors while all the remaining terms were random factors. eTotal number of significant genes with TST-FDR adjusted p ≤ 0.01. fPercentage of the total number of detectable genes that are significant. gNumber of significant genes found with both Wilcoxon and LMMA. hThe number of matches found with both methods, as a percentage of the total number of significant genes found by Wilcoxon or LMMA, whichever was smaller.