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Motivation: We describe an approach to normalize spotted microarray data, based on a physically motivated calibration model. This model consists of two major components, describing the hybridization of target transcripts to their corresponding probes on the one hand, and the measurement of fluorescence from the hybridized, labeled target on the other hand. The model parameters and error distributions are estimated from external control spikes. Results: Using a publicly available dataset, wedoi:10.1093/bioinformatics/btl068 pmid:16522672 fatcat:zkb4burb6fa55pxnzmbtvr2r5m