Additional File 6.

Comparison of different normalization methods: Correlation of fold change in pair-wise tissues determined by Applied Biosystems microarrays and TaqMan® Gene Expression Assay based real-time PCR. Data on Liver vs. Lung samples are shown as a representative example. y-axis, fold change determined by microarrays which is defined as: log2 (MedianSignal_tissue1/MedianSignal_tissue2); x-axis, fold change determined by real-time PCR, which is defined as ΔΔCt = (Ct_tissue2-Ct_PPIA)-(Ct_tissue1-Ct_PPIA). Genes were filtered based on real-time PCR detection thresholds (detectable in at least 3 out of 4 technical replicates in each tissue and detectable in both tissues, the number of genes are shown in the parentheses). A robust linear regression fitting and the corresponding R2 value are presented in each plot. Different normalization methods showed little difference in fold change correlation with TaqMan assays.

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Wang et al. BMC Genomics 2006 7:59   doi:10.1186/1471-2164-7-59