{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,6]],"date-time":"2026-03-06T13:04:56Z","timestamp":1772802296825,"version":"3.50.1"},"reference-count":20,"publisher":"Oxford University Press (OUP)","issue":"7","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2006,4,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: In the Affymetrix GeneChip system, preprocessing occurs before one obtains expression level measurements. Because the number of competing preprocessing methods was large and growing we developed a benchmark to help users identify the best method for their application. A webtool was made available for developers to benchmark their procedures. At the time of writing over 50 methods had been submitted.<\/jats:p>\n               <jats:p>Results: We benchmarked 31 probe set algorithms using a U95A dataset of spike in controls. Using this dataset, we found that background correction, one of the main steps in preprocessing, has the largest effect on performance. In particular, background correction appears to improve accuracy but, in general, worsen precision. The benchmark results put this balance in perspective. Furthermore, we have improved some of the original benchmark metrics to provide more detailed information regarding precision and accuracy. A handful of methods stand out as providing the best balance using spike-in data with the older U95A array, although different experiments on more current arrays may benchmark differently.<\/jats:p>\n               <jats:p>Availability: The affycomp package, now version 1.5.2, continues to be available as part of the Bioconductor project (). The webtool continues to be available at<\/jats:p>\n               <jats:p>Contact: \u00a0rafa@jhu.edu<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btk046","type":"journal-article","created":{"date-parts":[[2006,1,13]],"date-time":"2006-01-13T01:54:20Z","timestamp":1137117260000},"page":"789-794","source":"Crossref","is-referenced-by-count":228,"title":["Comparison of Affymetrix GeneChip expression measures"],"prefix":"10.1093","volume":"22","author":[{"given":"Rafael A.","family":"Irizarry","sequence":"first","affiliation":[{"name":"Department of Biostatistics, Johns Hopkins University 1 \u00a0 1 \u00a0 \u00a0 615 N. Wolfe Street, Baltimore, MD 21205, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Zhijin","family":"Wu","sequence":"additional","affiliation":[{"name":"Center for Statistical Sciences, Department of Community Health, Brown University 2 \u00a0 2 \u00a0 \u00a0 167 Angell Street, BOX G-H, Providence, RI 02912, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Harris A.","family":"Jaffee","sequence":"additional","affiliation":[{"name":"Department of Biostatistics, Johns Hopkins University 1 \u00a0 1 \u00a0 \u00a0 615 N. Wolfe Street, Baltimore, MD 21205, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2006,1,12]]},"reference":[{"key":"2023012409121841900_b1","article-title":"Statistical algorithms description document","volume-title":"Technical report","author":"Affymetrix","year":"2002"},{"key":"2023012409121841900_b2","doi-asserted-by":"crossref","first-page":"95","DOI":"10.1089\/106652703763255697","article-title":"Contrast normalization of oligonucleotide arrays","volume":"10","author":"\u00c5strand","year":"2003","journal-title":"J. Comput. Biol."},{"key":"2023012409121841900_b3","doi-asserted-by":"crossref","first-page":"R16","DOI":"10.1186\/gb-2005-6-2-r16","article-title":"Preferred analysis methods for Affymetrix GeneChips revealed by a wholly defined control dataset","volume":"6","author":"Choe","year":"2005","journal-title":"Geneome Biol"},{"key":"2023012409121841900_b4","doi-asserted-by":"crossref","first-page":"323","DOI":"10.1093\/bioinformatics\/btg410","article-title":"A benchmark for Affymetrix Genechip expression measures","volume":"20","author":"Cope","year":"2004","journal-title":"Bioinformatics"},{"key":"2023012409121841900_b5","first-page":"62P10","article-title":"A mixed model expression index to summarize affymetrix geneChip probe level data","volume":"62-07","author":"Deng","year":"2005","journal-title":"Mathematical Subject Classification"},{"key":"2023012409121841900_b6","doi-asserted-by":"crossref","first-page":"S105","DOI":"10.1093\/bioinformatics\/18.suppl_1.S105","article-title":"A variance-stabilizing transformation for gene-expression microarray data","volume":"18","author":"Durbin","year":"2002","journal-title":"Bioinformatics"},{"key":"2023012409121841900_b7","article-title":"Comparison of background correction and normalization procedures for high-density oligonucleotide microarrays","volume-title":"Technical Report 3, Leipzig Bioinformatics Working Paper","author":"Freudenberg","year":"2005"},{"key":"2023012409121841900_b8","doi-asserted-by":"crossref","first-page":"1231","DOI":"10.1016\/S0002-9440(10)62509-6","article-title":"Organ-specific molecular classification of primary lung, colon, and ovarian adenocarcinomas using gene expression profiles","volume":"159","author":"Giordano","year":"2001","journal-title":"Am. 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Pathol."},{"key":"2023012409121841900_b9","article-title":"Supplemental data: robust estimators for expression analysis","author":"Hubbell"},{"key":"2023012409121841900_b10","doi-asserted-by":"crossref","first-page":"S96","DOI":"10.1093\/bioinformatics\/18.suppl_1.S96","article-title":"Variance stabilization applied to microarray data calibration and to the quantification of differential expression","volume":"18","author":"Huber","year":"2002","journal-title":"Bioinformatics"},{"key":"2023012409121841900_b11","doi-asserted-by":"crossref","first-page":"249","DOI":"10.1093\/biostatistics\/4.2.249","article-title":"Exploration, normalization, and summaries of high density oligonucleotide array probe level data","volume":"4","author":"Irizarry","year":"2003","journal-title":"Biostatistics"},{"key":"2023012409121841900_b12","doi-asserted-by":"crossref","first-page":"163","DOI":"10.1109\/TNB.2003.817020","article-title":"Algorithm to model gene expression on affymetrix chips without the use of mm cells","volume":"2","author":"Lauren","year":"2003","journal-title":"IEEE Trans. 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