{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,9,20]],"date-time":"2025-09-20T19:23:39Z","timestamp":1758396219482},"reference-count":19,"publisher":"Oxford University Press (OUP)","issue":"19","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2006,10,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: The need for normalization in microarray experiments has been well documented in the literature. Currently, many analysis methods treat normalization and analysis as a series of steps, with summarized data carried forward to the next step.<\/jats:p>\n               <jats:p>Results: We present a unified algorithm which incorporates normalization and class comparison in one analysis using probe level perfect match and mismatch data. The algorithm is based on calibration models common to most biological assays, and the resulting chip-specific parameters have a natural interpretation. We show that the algorithm fits into the statistical generalized linear models framework, describe a practical fitting strategy and present results of the algorithm applied to an example dataset as well as based on metrics used in affycomp. The algorithm ranks amongst the top third of the affycomp competitors, performing best in measures of bias.<\/jats:p>\n               <jats:p>Availability: R functions are available on request from the authors.<\/jats:p>\n               <jats:p>Contact: \u00a0oberg.ann@mayo.edu<\/jats:p>","DOI":"10.1093\/bioinformatics\/btl399","type":"journal-article","created":{"date-parts":[[2006,7,30]],"date-time":"2006-07-30T18:13:51Z","timestamp":1154283231000},"page":"2381-2387","source":"Crossref","is-referenced-by-count":4,"title":["Joint estimation of calibration and expression for high-density oligonucleotide arrays"],"prefix":"10.1093","volume":"22","author":[{"given":"Ann L.","family":"Oberg","sequence":"first","affiliation":[{"name":"Division of Biostatistics, Department of Health Sciences Research, Mayo Clinic College of Medicine \u00a0 200 First Street SW, Rochester, MN 55905, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Douglas W.","family":"Mahoney","sequence":"additional","affiliation":[{"name":"Division of Biostatistics, Department of Health Sciences Research, Mayo Clinic College of Medicine \u00a0 200 First Street SW, Rochester, MN 55905, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Karla V.","family":"Ballman","sequence":"additional","affiliation":[{"name":"Division of Biostatistics, Department of Health Sciences Research, Mayo Clinic College of Medicine \u00a0 200 First Street SW, Rochester, MN 55905, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Terry M.","family":"Therneau","sequence":"additional","affiliation":[{"name":"Division of Biostatistics, Department of Health Sciences Research, Mayo Clinic College of Medicine \u00a0 200 First Street SW, Rochester, MN 55905, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2006,7,28]]},"reference":[{"key":"2023012409245218500_b1","doi-asserted-by":"crossref","first-page":"794","DOI":"10.1182\/blood-2004-04-1424","article-title":"Functional gene expression analysis of clonal plasma cells identifies a unique molecular profile for light chain amyloidosis","volume":"105","author":"Abraham","year":"2005","journal-title":"Blood"},{"key":"2023012409245218500_b2","article-title":"Microarray suite user guide, version 5","author":"Affymetrix","year":"2001"},{"key":"2023012409245218500_b3","article-title":"An exploration of affymetrix probe-set intensities in spike-in experiments","author":"Ballman","year":"2005"},{"key":"2023012409245218500_b4","doi-asserted-by":"crossref","first-page":"2778","DOI":"10.1093\/bioinformatics\/bth327","article-title":"Faster cyclic loess: normalizing RNA arrays via linear models","volume":"20","author":"Ballman","year":"2004","journal-title":"Bioinformatics"},{"key":"2023012409245218500_b5","doi-asserted-by":"crossref","first-page":"185","DOI":"10.1093\/bioinformatics\/19.2.185","article-title":"A comparison of normalization methods for high-density oligonucleotide array data based on variance and bias","volume":"19","author":"Bolstad","year":"2003","journal-title":"Bioinformatics"},{"key":"2023012409245218500_b6","doi-asserted-by":"crossref","DOI":"10.2202\/1544-6115.1095","article-title":"Statistical analysis of adsorption models for oligonucleotide microarrays","volume":"3","author":"Burden","year":"2004","journal-title":"Stat Appl. 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Soft Matter Phys."},{"key":"2023012409245218500_b17","doi-asserted-by":"crossref","first-page":"178","DOI":"10.1093\/bioinformatics\/19.2.178","article-title":"A study of accuracy and precision in oligonucleotide arrays: extracting more signal at large concentrations","volume":"19","author":"Naef","year":"2003","journal-title":"Bioinformatics"},{"key":"2023012409245218500_b18","article-title":"Stochastic models inspired by hybridization theory for short oligonucleotide arrays [extended abstract]","author":"Wu","year":"2004"},{"key":"2023012409245218500_b19","doi-asserted-by":"crossref","first-page":"909","DOI":"10.1198\/016214504000000683","article-title":"A model-based background adjustment for oligonucleotide expression arrays","volume":"99","author":"Wu","year":"2004","journal-title":"J. Am. Stat. 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