Sensitivity and specificity in detection of differential expression at different expression levels. For each platform, significantly differentially expressed genes for any given pair-wise tissues are determined as p-value < 0.05 using a student t-test (Panel A), using p-value adjusted according to Benjamini Horschberg multiple testing to control FDR at 5% (Panel B), or using a fold change cutoff (> 1.2-fold) for the TaqMan reference data sets while using a fold change cutoff (> 1.2-fold) and p-value < 0.05 based on t-test for microarray platforms (Panel C). Composite results for all three pairs of tissues (Brain vs. Liver, Brain vs. Lung, and Liver vs. Lung) were plotted. Gene expression levels are ordered according to TaqMan® Gene Expression Assay measurements (average Ct between the three tissues, only genes detected in both tissues by TaqMan assays were analyzed). A sliding window containing 100 consecutive genes was constructed and moved one gene at a time to cover the whole range of Ct values. Within each sliding window, the True Positive Rate (upper panel) and False Discovery Rate (lower panel) of each microarray platform was computed and plotted as a function of gene expression level.
Wang et al. BMC Genomics 2006 7:59 doi:10.1186/1471-2164-7-59