{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,23]],"date-time":"2026-02-23T23:46:44Z","timestamp":1771890404424,"version":"3.50.1"},"reference-count":26,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2004,11,12]],"date-time":"2004-11-12T00:00:00Z","timestamp":1100217600000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/2.0\/"},{"start":{"date-parts":[[2004,11,12]],"date-time":"2004-11-12T00:00:00Z","timestamp":1100217600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/2.0\/"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"abstract":"<jats:title>Abstract<\/jats:title><jats:sec>\n                        <jats:title>Background<\/jats:title>\n                        <jats:p>Non-linearities in observed log-ratios of gene expressions, also known as intensity dependent log-ratios, can often be accounted for by global biases in the two channels being compared. Any step in a microarray process may introduce such offsets and in this article we study the biases introduced by the microarray scanner and the image analysis software.<\/jats:p>\n                     <\/jats:sec><jats:sec>\n                        <jats:title>Results<\/jats:title>\n                        <jats:p>By scanning the same spotted oligonucleotide microarray at different photomultiplier tube (PMT) gains, we have identified a channel-specific bias present in two-channel microarray data. For the scanners analyzed it was in the range of 15\u201325 (out of 65,535). The observed bias was very stable between subsequent scans of the same array although the PMT gain was greatly adjusted. This indicates that the bias does not originate from a step preceding the scanner detector parts. The bias varies slightly between arrays. When comparing estimates based on data from the same array, but from different scanners, we have found that different scanners introduce different amounts of bias. So do various image analysis methods. We propose a scanning protocol and a constrained affine model that allows us to identify and estimate the bias in each channel. Backward transformation removes the bias and brings the channels to the same scale. The result is that systematic effects such as intensity dependent log-ratios are removed, but also that signal densities become much more similar. The average scan, which has a larger dynamical range and greater signal-to-noise ratio than individual scans, can then be obtained.<\/jats:p>\n                     <\/jats:sec><jats:sec>\n                        <jats:title>Conclusions<\/jats:title>\n                        <jats:p>The study shows that microarray scanners may introduce a significant bias in each channel. Such biases have to be calibrated for, otherwise systematic effects such as intensity dependent log-ratios will be observed. The proposed scanning protocol and calibration method is simple to use and is useful for evaluating scanner biases or for obtaining calibrated measurements with extended dynamical range and better precision. The cross-platform R package aroma, which implements all described methods, is available for free from <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"http:\/\/www.maths.lth.se\/bioinformatics\/\">http:\/\/www.maths.lth.se\/bioinformatics\/<\/jats:ext-link>.<\/jats:p>\n                     <\/jats:sec>","DOI":"10.1186\/1471-2105-5-177","type":"journal-article","created":{"date-parts":[[2004,11,18]],"date-time":"2004-11-18T09:53:33Z","timestamp":1100771613000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":32,"title":["Calibration and assessment of channel-specific biases in microarray data with extended dynamical range"],"prefix":"10.1186","volume":"5","author":[{"given":"Henrik","family":"Bengtsson","sequence":"first","affiliation":[]},{"given":"G\u00f6ran","family":"J\u00f6nsson","sequence":"additional","affiliation":[]},{"given":"Johan","family":"Vallon-Christersson","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2004,11,12]]},"reference":[{"issue":"1 Supplement","key":"293_CR1","doi-asserted-by":"publisher","first-page":"10","DOI":"10.1038\/4434","volume":"21","author":"DJ Duggan","year":"1999","unstructured":"Duggan DJ, Bittner M, Chen Y, Meltzer P, Trent JM: Expression profiling using cDNA microarrays.\n                           Nature Genetics 1999, 21(1 Supplement):10\u201314. 10.1038\/4434","journal-title":"Nature Genetics"},{"key":"293_CR2","volume-title":"Preprints in Mathematical Sciences 2003:38, Mathematical Statistics, Centre for Mathematical Sciences, Lund University, Sweden","author":"H Bengtsson","year":"2003","unstructured":"Bengtsson H, H\u00f6ssjer O: Methodological study of affine transformations of gene expression data with proposed normalization method.\n                           Preprints in Mathematical Sciences 2003:38, Mathematical Statistics, Centre for Mathematical Sciences, Lund University, Sweden 2003, in press."},{"key":"293_CR3","volume-title":"Tech rep, The Jackson Laboratory, USA","author":"X Cui","year":"2002","unstructured":"Cui X, Kerr MK, Churchill GA: Data Transformations for cDNA Microarray Data.\n                           Tech rep, The Jackson Laboratory, USA 2002."},{"key":"293_CR4","volume-title":"Lancaster, PA, U S A","author":"Burle Industries Inc","year":"1980","unstructured":"Burle Industries Inc: Photomultiplier Handbook.\n                           Lancaster, PA, U S A 1980."},{"key":"293_CR5","volume-title":"Technical Report 578, Department of Statistics, University of California at Berkeley","author":"S Dudoit","year":"2000","unstructured":"Dudoit S, Yang YH, Callow MJ, Speed TP: Statistical methods for identifying differentially expressed genes in replicated cDNA microarray experiments.\n                           Technical Report 578, Department of Statistics, University of California at Berkeley 2000."},{"key":"293_CR6","first-page":"141","volume-title":"In Proceedings of SPiE, Volume 4266 of Microarrays: Optical Technologies and Informatics","author":"YH Yang","year":"2001","unstructured":"Yang YH, Dudoit S, Luu P, Speed TP: Normalization for cDNA microarray data. In In Proceedings of SPiE, Volume 4266 of Microarrays: Optical Technologies and Informatics. Edited by: Bittner ML, Chen Y, Dorsel AN, Dougherty ER, San Jose. California: The International Society for Optical Engineering; 2001:141\u2013152."},{"issue":"Suppl 1","key":"293_CR7","doi-asserted-by":"publisher","first-page":"S96","DOI":"10.1093\/bioinformatics\/18.suppl_1.S96","volume":"18","author":"W Huber","year":"2002","unstructured":"Huber W, von Heydebreck A, S\u00fcltmann H, Poustka A, Vingron M: Variance stabilization applied to microarray data calibration and to the quantification of differential expression.\n                           Bioinformatics 2002, 18(Suppl 1):S96\u2013104.","journal-title":"Bioinformatics"},{"key":"293_CR8","volume-title":"Technical Report 584, Department of Statistics, University of California at Berkeley","author":"YH Yang","year":"2000","unstructured":"Yang YH, Buckley M, Dudoit S, Speed T: Comparison of methods for image analysis on cDNA microarray data.\n                           Technical Report 584, Department of Statistics, University of California at Berkeley 2000."},{"key":"293_CR9","volume-title":"Master's Theses in Mathematical Sciences, Mathematical Statistics, Centre for Mathematical Sciences, Lund Institute of Technology, Sweden","author":"A Bengtsson","year":"2003","unstructured":"Bengtsson A: Microarray Image Analysis: Background Estimation using Region and Filtering Techniques.\n                           Master's Theses in Mathematical Sciences, Mathematical Statistics, Centre for Mathematical Sciences, Lund Institute of Technology, Sweden 2003."},{"issue":"20","key":"293_CR10","doi-asserted-by":"publisher","first-page":"12975","DOI":"10.1073\/pnas.162468199","volume":"99","author":"JP Brody","year":"2002","unstructured":"Brody JP, Williams BA, Wold BJ, Quake SR: Significance and statistical errors in the analysis of DNA microarray data.\n                           Proc Natl Acad Sci U S A 2002, 99(20):12975\u201312978. 10.1073\/pnas.162468199","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"6","key":"293_CR11","doi-asserted-by":"publisher","first-page":"557","DOI":"10.1089\/106652701753307485","volume":"8","author":"DM Rocke","year":"2001","unstructured":"Rocke DM, Durbin B: A Model for Measurement Error for Gene Expression Arrays.\n                           Journal of Computational Biology 2001, 8(6):557\u2013569. 10.1089\/106652701753307485","journal-title":"Journal of Computational Biology"},{"key":"293_CR12","doi-asserted-by":"publisher","first-page":"55","DOI":"10.1089\/10665270252833190","volume":"9","author":"C Kooperberg","year":"2002","unstructured":"Kooperberg C, Fazzio TG, Delrow JJ, Tsukiyama T: Improved background correction for spotted DNA microarrays.\n                           Journal of Computational Biology 2002, 9: 55\u201366. 10.1089\/10665270252833190","journal-title":"Journal of Computational Biology"},{"key":"293_CR13","doi-asserted-by":"publisher","first-page":"1913","DOI":"10.1002\/sim.1013","volume":"21","author":"DM Hawkins","year":"2002","unstructured":"Hawkins DM: Diagnostics for conformity of paired quantitative measurements.\n                           Statistics in Medicine 2002, 21: 1913\u20131935. 10.1002\/sim.1013","journal-title":"Statistics in Medicine"},{"key":"293_CR14","doi-asserted-by":"publisher","first-page":"S105","DOI":"10.1093\/bioinformatics\/18.suppl_1.S105","volume":"18","author":"B Durbin","year":"2002","unstructured":"Durbin B, Hardin J, Hawkins D, Rocke D: A variance-stabilizing transformation for gene-expression microarray data.\n                           Bioinformatics 2002, 18: S105-S110.","journal-title":"Bioinformatics"},{"issue":"2","key":"293_CR15","doi-asserted-by":"publisher","first-page":"185","DOI":"10.1093\/bioinformatics\/19.2.185","volume":"19","author":"B Bolstad","year":"2003","unstructured":"Bolstad B, Irizarry R, \u00c5strand M, Speed T: A comparison of normalization methods for high density oligonucleotide array data based on variance and bias.\n                           Bioinformatics 2003, 19(2):185\u201393. 10.1093\/bioinformatics\/19.2.185","journal-title":"Bioinformatics"},{"key":"293_CR16","doi-asserted-by":"publisher","first-page":"403","DOI":"10.1214\/lnms\/1215091155","volume-title":"In Science and Statistics: A Festschrift for Terry Speed, Volume 40 of Monograph Series","author":"YH Yang","year":"2003","unstructured":"Yang YH, Thorne NP: Normalization for Two-color cDNA Microarray Data. 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