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. 2012 Aug 30;7(8):e44357. doi: 10.1371/journal.pone.0044357

Table 2. ANOVA results tables for tests for differences in OTU diversity among two main treatment effects.

OTU diversity (Shannon index) ∼ Plant richness * Host species
AmpliconNoise processed
Source DF Sum of Squares Mean Square F Value Pr>F
Model 19 2.66 0.14 3.35 0.0009 **
Error 35 1.46 0.042
Corrected Total 54 4.12
DF Type III SS MS F Pr>F
Richness 4 1.17 0.29 6.99 0.0028 **
Species 3 0.38 0.13 3.02 0.042 *
Diversity*Species 12 1.53 0.13 3.07 0.0048 **
Standard processed
Source DF SS MS F Pr>F
Model 19 1.78 0.094 1.74 0.077 .
Error 35 1.89 0.054
Corrected Total 54 3.67
DF Type III SS MS F Pr>F
Richness 4 0.76 0.19 3.53 0.016 *
Species 3 0.32 0.11 2.01 0.13
Diversity*Species 12 0.89 0.074 1.37 0.22

We contrast the significance of differences when the underlying data is processed through AmpliconNoise (top) vs. through a standard pipeline (bottom).