SMART has the highest true-positive rate of differentially expressed genes across a range of empirical thresholds. The outliers for each amplification method were selected for four 3T3 vs OV hybridizations (two replicates and two dye swaps) with cutoff levels as a fixed number of genes with the highest LOD scores: 1,000, 500, and 100. The number of true-positive outliers was calculated by intersecting the set of outliers at each given threshold level for each amplification technique with the set of outliers selected for unamplified targets. The total number of selected outliers for each amplification at a given threshold was designated as 100%. The LOD scores therefore varied depending on cutoff level and type of amplification (see also Table 3). IVTIII, T7-based linear amplification; GA, global polyadenylated PCR amplification; SMART, SMART PCR amplification; SM37, modified SMART amplification.
Subkhankulova and Livesey Genome Biology 2006 7:R18 doi:10.1186/gb-2006-7-3-r18