%0 Journal Article %1 Wu:2004:a %A Wu, Zhijin %A Irizarry, Rafael A %D 2004 %J Nature Biotechnology %K array expression preprocessing %N 6 %P 656--658 %T Preprocessing of oligonucleotide array data %U http://www.nature.com/nbt/journal/v22/n6/full/nbt0604-656b.html %V 22 %X A paper by Zhang et al. 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.

@article{Wu:2004:a, abstract = {A paper by Zhang et al. 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.}, added-at = {2007-10-23T13:35:30.000+0200}, author = {Wu, Zhijin and Irizarry, Rafael A}, biburl = {https://www.bibsonomy.org/bibtex/2b4261adae03b96c0ee142a0529542902/tkirsten}, interhash = {fed5fda5ad31ae0a6c57d8411656b78e}, intrahash = {b4261adae03b96c0ee142a0529542902}, journal = {Nature Biotechnology}, keywords = {array expression preprocessing}, number = 6, owner = {tkirsten}, pages = {656--658}, timestamp = {2007-10-23T13:50:34.000+0200}, title = {{Preprocessing of oligonucleotide array data}}, url = {http://www.nature.com/nbt/journal/v22/n6/full/nbt0604-656b.html}, volume = 22, year = 2004 }