Additional file 6.

Determination of the cutoff RPKM value for expressed genes by comparing microarray and RNA-seq data. The histogram shows the distribution of RPKMs for genes that are unambiguously called 'Present' in all three replicates from the gene expression microarray data. The RPKM values are adjusted by adding a pseudo-count of 1 prior to the logarithm. Threshold RPKM values of 0.5 and 1 are shown as dashed lines in blue and green, respectively. Approximately 99% of genes that are considered unambiguously 'Present' (3P calls) in the microarray data have an RPKM ≥ 1. Therefore, we assigned RPKM ≥ 1 as the cutoff for expressed genes. Conversely, only 0.4% of these genes have an RPKM < 0.5, and we assigned RPKM < 0.5 as the cutoff for absent or silent genes.

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Gan et al. Genome Biology 2010 11:R42   doi:10.1186/gb-2010-11-4-r42