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Table 2 Number of significant genes for the poppy data

From: Separate-channel analysis of two-channel microarrays: recovering inter-spot information

    Number of differentially expressed genes
Analysis Comparison π ̂ 0 FDR <0.05 FDR <0.01
Log-ratio Leaf vs Sepal 0.52 1157 668
Separate channel Leaf vs Sepal 0.64 1331 954
Log-ratio Leaf vs Carpel 0.84 254 132
Separate channel Leaf vs Carpel 0.87 505 314
  1. Rows give results for different tissue comparisons and different analysis methods. The column π ̂ 0 gives the estimated proportion of probes that are not differentially expressed between the tissue types. FDRs and π0 values were estimated using the qvalue package. The separate channel method detects more significant genes but does not decrease π ̂ 0 overall.