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Preprocessing of oligonucleotide array data

Nature Biotechnology volume 22, pages 656–658 (2004)Cite this article

To the editor:

A paper by Zhang et al.1 in the July 2003 issue of Nature Biotechnology presents PerfectMatch, a physical-model-based algorithm for modeling the binding interactions between probes on Affymetrix (Santa Clara, CA, USA) GeneChip oligonucleotide arrays and their target nucleic acids. Stochastic-model-based algorithms have been shown to improve the preprocessing of array data to take into account the presence of optical noise, nonspecific binding and probe-specific effects. Although Zhang et al. demonstrate the superior performance of PerfectMatch over two widely used algorithms, MAS 5.0 and dChip, they fail to consider a leading stochastic-model-based procedure, robust multi-array analysis (RMA), from our group2. Here, we provide evidence that (i) measurements obtained using RMA are as precise and more accurate than those obtained using PerfectMatch and (ii) the accuracy of stochastic-model-based procedures can be improved by carefully incorporating physical model information.

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Figure 1: Graphical comparison of the capacity of four algorithms (MAS 5.0, PerfectMatch, RMA and GCRMA) to measure expression.

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Authors and Affiliations

  1. Department of Biostatistics, Bloomberg School of Public Health, Johns Hopkins University, 615 North Wolfe Street, Baltimore, 21205, Maryland, USA

    Zhijin Wu & Rafael A Irizarry

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  1. Zhijin Wu
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  2. Rafael A Irizarry
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Wu, Z., Irizarry, R. Preprocessing of oligonucleotide array data. Nat Biotechnol 22, 656–658 (2004). https://doi.org/10.1038/nbt0604-656b

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