Estimating relative transcript abundance. (a) Comparison of transcript levels estimated either directly by hybridization of prostate sample mRNA versus normal female genomic DNA, or indirectly by multiplying the ratio of prostate sample mRNA vs common reference mRNA by the ratio of common reference mRNA vs normal female genomic DNA. The correlation value (R) is indicated. (b) Prostate-specific gene-expression cluster, extracted from the hierarchical cluster shown in Figure 1a, is displayed as mean-centered relative gene expression (ratio-fold change scale indicated). (c) The same gene-expression feature as in (b), is now displayed as transcript abundance (relative to the average transcript level for all expressed genes), calculated indirectly using the common reference mRNA versus normal female genomic DNA hybridization data.