Figure 5

Precision-Recall curves for spiked Gene ST measurements. Here, artefacts were projected from the exon array measurements onto the gene arrays to produce realistic noise patterns. Three different scoring approaches were compared both for the simple threshold approach, the ε-criterion (a), and its cumulative variant, the window-criterion (b), which takes into account the probe neighborhood information. The scoring approaches compared are: (i) absolute log fold change between total RNA and normalized sum of newly transcribed and pre-existing RNA (fold change (T/N + P), see Methods); (ii) absolute log fold change between replicates (fold change replicates); (iii) residuals determined with the RMA summarization approach using the affyPLM model (affyPLM). These results show that the window-based approach improves the performance of all used methods, resulting in almost identical performance for all of them, which is superior to the performance of both Harshlight and MBR.