{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,30]],"date-time":"2026-05-30T03:05:51Z","timestamp":1780110351699,"version":"3.54.0"},"reference-count":19,"publisher":"Oxford University Press (OUP)","issue":"1","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2008,1,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: In two-color microarray experiments, well-known differences exist in the labeling and hybridization efficiency of Cy3 and Cy5 dyes. Previous reports have revealed that these differences can vary on a gene-by-gene basis, an effect termed gene-specific dye bias. If uncorrected, this bias can influence the determination of differentially expressed genes.<\/jats:p>\n               <jats:p>Results: We show that the magnitude of the bias scales multiplicatively with signal intensity and is dependent on which nucleotide has been conjugated to the fluorescent dye. A method is proposed to account for gene-specific dye bias within a maximum-likelihood error modeling framework. Using two different labeling schemes, we show that correcting for gene-specific dye bias results in the superior identification of differentially expressed genes within this framework. Improvement is also possible in related ANOVA approaches.<\/jats:p>\n               <jats:p>Availability: A software implementation of this procedure is freely available at http:\/\/cellcircuits.org\/VERA<\/jats:p>\n               <jats:p>Contact: \u00a0rmkelley@ucsd.edu<\/jats:p>\n               <jats:p>Supplementary information: Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btm347","type":"journal-article","created":{"date-parts":[[2007,7,11]],"date-time":"2007-07-11T01:44:07Z","timestamp":1184118247000},"page":"71-77","source":"Crossref","is-referenced-by-count":10,"title":["Correcting for gene-specific dye bias in DNA microarrays using the method of maximum likelihood"],"prefix":"10.1093","volume":"24","author":[{"given":"Ryan","family":"Kelley","sequence":"first","affiliation":[{"name":"1 Program in Bioinformatics and 2Department of Bioengineering, University of California, San Diego 9500 Gilman Drive, La Jolla, CA 92093-0412, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hoda","family":"Feizi","sequence":"additional","affiliation":[{"name":"1 Program in Bioinformatics and 2Department of Bioengineering, University of California, San Diego 9500 Gilman Drive, La Jolla, CA 92093-0412, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Trey","family":"Ideker","sequence":"additional","affiliation":[{"name":"1 Program in Bioinformatics and 2Department of Bioengineering, University of California, San Diego 9500 Gilman Drive, La Jolla, CA 92093-0412, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2007,7,10]]},"reference":[{"key":"2023020209470638200_B1","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":"2023020209470638200_B2","doi-asserted-by":"crossref","first-page":"59","DOI":"10.1093\/biostatistics\/kxh018","article-title":"Improved statistical tests for differential gene expression by shrinking variance components estimates","volume":"6","author":"Cui","year":"2005","journal-title":"Biostatistics"},{"key":"2023020209470638200_B3","doi-asserted-by":"crossref","first-page":"502","DOI":"10.1093\/bioinformatics\/bti023","article-title":"VarMixt: efficient variance modelling for the differential analysis of replicated gene expression data","volume":"21","author":"Delmar","year":"2005","journal-title":"Bioinformatics"},{"key":"2023020209470638200_B4","doi-asserted-by":"crossref","first-page":"2430","DOI":"10.1093\/bioinformatics\/bti378","article-title":"Characterizing dye bias in microarray experiments","volume":"21","author":"Dobbin","year":"2005","journal-title":"Bioinformatics"},{"key":"2023020209470638200_B5","doi-asserted-by":"crossref","first-page":"120","DOI":"10.1016\/S0014-5793(04)00083-3","article-title":"Gene-specific dye bias in microarray reference designs","volume":"560","author":"Dombkowski","year":"2004","journal-title":"FEBS Lett"},{"key":"2023020209470638200_B6","doi-asserted-by":"crossref","first-page":"1962","DOI":"10.1093\/nar\/gkg283","article-title":"Absolute mRNA concentrations from sequence-specific calibration of oligonucleotide arrays","volume":"31","author":"Hekstra","year":"2003","journal-title":"Nucleic Acids Res"},{"key":"2023020209470638200_B7","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":"2023020209470638200_B8","doi-asserted-by":"crossref","first-page":"805","DOI":"10.1089\/10665270050514945","article-title":"Testing for differentially-expressed genes by maximum-likelihood analysis of microarray data","volume":"7","author":"Ideker","year":"2000","journal-title":"J. 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