Table 2.

Number of significant genes for the poppy data

			Number of differentially expressed genes
Analysis	Comparison	$${\widehat{\mathbf{\pi }}}_{\mathbf{0}}$$	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

Rows give results for different tissue comparisons and different analysis methods. The column ${\widehat{\pi }}_0$ 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${\widehat{\pi }}_0$ overall.