Figure 4

Filtering by variance using different thresholds for wheat case study and simulation study. Plot (A) is the observed power of one run of simulation (independent case with π₀ = 0.8 represented by the vertical dashed line) found when filtering by variance using different variance quantiles (0.05 to 0.95) as thresholds and controlling FDR at α = 0.05. Plot (B) is the observed FDR of the same simulation run found when filtering by variance using different variance quantiles. The horizontal dashed line represents the nominal FDR. Plot (C) is the number of differentially expressed genes (DEGs) identified for Wheat comparison 1 (using RMA preprocessing) and filtering by variance (on the log₂ scale) using different variance quantiles (0.05 to 0.95) as thresholds. The vertical dashed line represents the q-value estimate of the proportion of null hypotheses ($\widehat{\pi }$₀ = 0.62).