A benchmark for Affymetrix GeneChip expression measures
作者： L. M. Cope , R. A. Irizarry , H. A. Jaffee , Z. Wu , T. P. Speed
DOI: 10.1093/BIOINFORMATICS/BTG410
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摘要: Motivation: The defining feature of oligonucleotide expression arrays is the use several probes to assay each targeted transcript. This a bonanza for statistical geneticist, who can create probeset summaries with specific characteristics. There are now methods available summarizing probe level data from popular Affymetrix GeneChips, but it difficult identify best method given inquiry. Results: We have developed graphical tool evaluate data. Plots and summary statistics offer picture how an measure performs in important areas. facilitates comparison competing measures selection suitable investigation. key benchmark set consisting dilution study spike-in study. Because truth known these data, we features which expected outcome advance. Those highlighted our suite graphs justified by questions biological interest motivated presence appropriate data. Availability: In conjunction release graphics toolbox as part Bioconductor project (http://www.bioconductor.org), webtool at http://affycomp.biostat.jhsph.edu. Supplemental material http://www.biostat.jhsph.edu/~ririzarr/papers/suppaffycomp.pdf
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