{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,28]],"date-time":"2026-03-28T08:15:02Z","timestamp":1774685702787,"version":"3.50.1"},"reference-count":32,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2007,5,1]],"date-time":"2007-05-01T00:00:00Z","timestamp":1177977600000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/2.0"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2007,12]]},"DOI":"10.1186\/1471-2105-8-142","type":"journal-article","created":{"date-parts":[[2007,5,2]],"date-time":"2007-05-02T11:24:05Z","timestamp":1178105045000},"source":"Crossref","is-referenced-by-count":155,"title":["Pre-processing Agilent microarray data"],"prefix":"10.1186","volume":"8","author":[{"given":"Marianna","family":"Zahurak","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Giovanni","family":"Parmigiani","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Wayne","family":"Yu","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Robert B","family":"Scharpf","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"David","family":"Berman","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Edward","family":"Schaeffer","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Shabana","family":"Shabbeer","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Leslie","family":"Cope","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2007,5,1]]},"reference":[{"key":"1514_CR1","doi-asserted-by":"publisher","first-page":"2549","DOI":"10.1093\/nar\/29.12.2549","volume":"29","author":"GC Tseng","year":"2001","unstructured":"Tseng GC, Oh MK, Rohlin L, Liao J, Wong W: Issues in cDNA microarray analysis: quality filtering, channel normalization, models of variations and assessment of gene effects. Nucleic Acids Research 2001, 29: 2549\u20132557. 10.1093\/nar\/29.12.2549","journal-title":"Nucleic Acids Research"},{"issue":"4","key":"1514_CR2","doi-asserted-by":"publisher","first-page":"e15","DOI":"10.1093\/nar\/30.4.e15","volume":"30","author":"YH Yang","year":"2002","unstructured":"Yang YH, Dudoit S, Luu P, Lin DM, Peng V, Ngai J, Speed T: Normalization for cDNA microarray data: A robust composite method addressing single and multiple slide systematic variation. Nucleic Acids Research 2002, 30(4):e15. 10.1093\/nar\/30.4.e15","journal-title":"Nucleic Acids Research"},{"key":"1514_CR3","first-page":"111","volume":"224","author":"G Smyth","year":"2003","unstructured":"Smyth G, Yang Y, Speed T: Statistical issues in cDNA microarray data analysis. Methods in Molecular Biology 2003, 224: 111\u2013136.","journal-title":"Methods in Molecular Biology"},{"key":"1514_CR4","doi-asserted-by":"publisher","first-page":"265","DOI":"10.1016\/S1046-2023(03)00155-5","volume":"31","author":"G Smyth","year":"2003","unstructured":"Smyth G, Speed T: Normalization of cDNA microarray data. Methods 2003, 31: 265\u2013273. 10.1016\/S1046-2023(03)00155-5","journal-title":"Methods"},{"key":"1514_CR5","volume-title":"The Analysis of Gene Expression Data: Methods and Software","author":"S Dudoit","year":"2003","unstructured":"Dudoit S, Yang J: Bioconductor R Packages for Exploratory Analysis and Normalization of cDNA Microarray Data. In The Analysis of Gene Expression Data: Methods and Software. Edited by: Parmigiani G, Garrett E, Irizarry R, Zeger S. New York: Springer Verlag; 2003."},{"key":"1514_CR6","doi-asserted-by":"publisher","first-page":"249","DOI":"10.1093\/biostatistics\/4.2.249","volume":"4","author":"RA Irizarry","year":"2003","unstructured":"Irizarry RA, Hobbs B, Collin F, Beazer-Barclay YD, Antonellis KJ, Scherf U, Speed TP: Exploration, Normalization, and Summaries of High Density Oligonucleotide Array Probe Level Data. Biostatistics 2003, 4: 249\u2013264. 10.1093\/biostatistics\/4.2.249","journal-title":"Biostatistics"},{"key":"1514_CR7","doi-asserted-by":"publisher","first-page":"120","DOI":"10.1117\/12.427980","volume-title":"SPIE Proceedings: Microarrays: Optical TEchnologies and Informatics 4266","author":"G Delenstarr","year":"2001","unstructured":"Delenstarr G, Cattel H, Chen C, Dorsel A, Kincaid R, Nguyen K, Sampas N, Schidel S, Shannon K, Tu A, Wolber P: Estimation ofthe confidence limits of oligo nucleotide array-based measurements of differential expression. SPIE Proceedings: Microarrays: Optical TEchnologies and Informatics 4266 2001, 120\u2013131."},{"key":"1514_CR8","volume-title":"R: A language and environment for statistical computing","author":"R Development Core Team","year":"2004","unstructured":"R Development Core Team:R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria; 2004. [ISBN 3\u2013900051\u201300\u20133] [\n                    http:\/\/www.R-project.org\n                    \n                  ] [ISBN 3-900051-00-3]"},{"key":"1514_CR9","volume-title":"Bioinformatics and Computational Biology Solutions Using R and Bioconductor","author":"G Smyth","year":"2005","unstructured":"Smyth G: limma: Linear Models for Microarray Data. In Bioinformatics and Computational Biology Solutions Using R and Bioconductor. Edited by: Gentleman R, Carey V, Huber W, Irizarry R, Dudoit S. New York: Springer Verlag; 2005."},{"issue":"18","key":"1514_CR10","doi-asserted-by":"publisher","first-page":"5471","DOI":"10.1093\/nar\/gkh866","volume":"32","author":"LX Qin","year":"2004","unstructured":"Qin LX, Kerr KF, the Toxicogenomics Research Consortium CM: Empirical evaluation of data transformations and ranking statistics for microarray analysis. Nucleic Acids Res 2004, 32(18):5471\u20135479. 10.1093\/nar\/gkh866","journal-title":"Nucleic Acids Res"},{"key":"1514_CR11","doi-asserted-by":"publisher","first-page":"R2+","DOI":"10.1186\/gb-2007-8-1-r2","volume":"8","author":"A Oshlack","year":"2007","unstructured":"Oshlack A, Emslie D, Corcoran L, Smyth GK: Normalization of boutique two-color microarrays with a high proportion of differentially expressed probes. Genome Biology 2007, 8: R2+. 10.1186\/gb-2007-8-1-r2","journal-title":"Genome Biology"},{"key":"1514_CR12","volume-title":"Bioinformatics and Computational Biology Solutions Using R and Bioconductor","author":"Y Yang","year":"2005","unstructured":"Yang Y, Paquet A: Preprocessing Two-Color Spotted Arrays. In Bioinformatics and Computational Biology Solutions Using R and Bioconductor. Edited by: Gentleman R, Carey V, Huber W, Irizarry R, Dudoit S. New York: Springer Verlag; 2005."},{"issue":"1\u20133","key":"1514_CR13","doi-asserted-by":"publisher","first-page":"120","DOI":"10.1016\/S0014-5793(04)00083-3","volume":"560","author":"AA Dombkowski","year":"2004","unstructured":"Dombkowski AA, Thibodeau BJ, Starcevic SL, Novak RF: Gene-specific dye bias in microarray reference designs. FEBS Lett 2004, 560(1\u20133):120\u2013124. 10.1016\/S0014-5793(04)00083-3","journal-title":"FEBS Lett"},{"issue":"10","key":"1514_CR14","doi-asserted-by":"publisher","first-page":"2430","DOI":"10.1093\/bioinformatics\/bti378","volume":"21","author":"KK Dobbin","year":"2005","unstructured":"Dobbin KK, Kawasaki ES, Petersen DW, Simon RM: Characterizing dye bias in microarray experiments. Bioinformatics 2005, 21(10):2430\u20132437. 10.1093\/bioinformatics\/bti378","journal-title":"Bioinformatics"},{"issue":"9","key":"1514_CR15","doi-asserted-by":"publisher","first-page":"1995","DOI":"10.1093\/bioinformatics\/bti302","volume":"21","author":"ML Martin-Magniette","year":"2005","unstructured":"Martin-Magniette ML, Aubert J, Cabannes E, Daudin JJ: Evaluation of the gene-specific dye bias in cDNA microarray experiments. Bioinformatics 2005, 21(9):1995\u20132000. 10.1093\/bioinformatics\/bti302","journal-title":"Bioinformatics"},{"issue":"4","key":"1514_CR16","doi-asserted-by":"publisher","first-page":"480","DOI":"10.1289\/ehp.6694","volume":"112","author":"BA Rosenzweig","year":"2004","unstructured":"Rosenzweig BA, Pine PS, Domon OE, Morris SM, Chen JJ, Sistare FD: Dye bias correction in dual-labeled cDNA microarray gene expression measurements. Environ Health Perspect 2004, 112(4):480\u2013487.","journal-title":"Environ Health Perspect"},{"issue":"7","key":"1514_CR17","doi-asserted-by":"publisher","first-page":"803","DOI":"10.1093\/bioinformatics\/btg076","volume":"19","author":"K Dobbin","year":"2003","unstructured":"Dobbin K, Shih JH, Simon R: Statistical design of reverse dye microarrays. Bioinformatics 2003, 19(7):803\u2013810. 10.1093\/bioinformatics\/btg076","journal-title":"Bioinformatics"},{"key":"1514_CR18","volume-title":"Agilent G2567AA Feature Extraction Software (v. 7.5)","author":"Agilent","year":"2004","unstructured":"Agilent: Agilent G2567AA Feature Extraction Software (v. 7.5). Agilent Technologies, Santa Clara, CA; 2004."},{"issue":"5","key":"1514_CR19","doi-asserted-by":"publisher","first-page":"351","DOI":"10.1038\/nmeth754","volume":"2","author":"T Bammler","year":"2005","unstructured":"Bammler T, Beyer RP, Bhattacharya S, Boorman GA, Boyles A, Bradford BU, Bumgarner RE, Bushel PR, Chaturvedi K, Choi D, Cunningham ML, Deng S, Dressman HK, Fannin RD, Farin FM, Freedman JH, Fry RC, Harper A, Humble MC, Hurban P, Kavanagh TJ, Kaufmann WK, Kerr KF, Jing L, Lapidus JA, Lasarev MR, Li J, Li YJ, Lobenhofer EK, Lu X, Malek RL, Milton S, Nagalla SR, O'malley JP, Palmer VS, Pattee P, Paules RS, Perou CM, Phillips K, Qin LX, Qiu Y, Quigley SD, Rodland M, Rusyn I, Samson LD, Schwartz DA, Shi Y, Shin JL, Sieber SO, Slifer S, Speer MC, Spencer PS, Sproles DI, Swenberg JA, Suk WA, Sullivan RC, Tian R, Tennant RW, Todd SA, Tucker CJ, Van Houten B, Weis BK, Xuan S, Zarbl Ha: Standardizing global gene expression analysis between laboratories and across platforms. Nat Methods 2005, 2(5):351\u2013356. 10.1038\/nmeth754","journal-title":"Nat Methods"},{"issue":"Suppl","key":"1514_CR20","doi-asserted-by":"publisher","first-page":"496","DOI":"10.1038\/ng1032","volume":"32","author":"J Quackenbush","year":"2002","unstructured":"Quackenbush J: Microarray data normalization and transformation. Nat Genet 2002, 32(Suppl):496\u2013501. 10.1038\/ng1032","journal-title":"Nat Genet"},{"issue":"4","key":"1514_CR21","doi-asserted-by":"publisher","first-page":"265","DOI":"10.1016\/S1046-2023(03)00155-5","volume":"31","author":"GK Smyth","year":"2003","unstructured":"Smyth GK, Speed T: Normalization of cDNA microarray data. Methods 2003, 31(4):265\u2013273. 10.1016\/S1046-2023(03)00155-5","journal-title":"Methods"},{"issue":"4","key":"1514_CR22","doi-asserted-by":"publisher","first-page":"e15","DOI":"10.1093\/nar\/30.4.e15","volume":"30","author":"YH Yang","year":"2002","unstructured":"Yang YH, Dudoit S, Luu P, Lin DM, Peng V, Ngai J, Speed TP: Normalization for cDNA microarray data: a robust composite method addressing single and multiple slide systematic variation. Nucleic Acids Res 2002, 30(4):e15. 10.1093\/nar\/30.4.e15","journal-title":"Nucleic Acids Res"},{"key":"1514_CR23","volume-title":"Biostatistics","author":"R Scharpf","year":"2006","unstructured":"Scharpf R, lacobuzio-Donahue C, JB S, Parmigiani G: When should one subtract background fluorescence in two color microarrays? Biostatistics 2006."},{"issue":"9","key":"1514_CR24","doi-asserted-by":"publisher","first-page":"1132","DOI":"10.1038\/nbt1237","volume":"24","author":"W Tong","year":"2006","unstructured":"Tong W, Lucas AB, Shippy R, Fan X, Fang H, Hong H, Orr MS, Chu TM, Guo X, Collins PJ, Sun YA, Wang SJ, Bao W, Wolfinger RD, Shchegrova S, Guo L, Warrington JA, Shi L: Evaluation of external RNA controls for the assessment of microarray performance. Nat Biotechnol 2006, 24(9):1132\u20131139. 10.1038\/nbt1237","journal-title":"Nat Biotechnol"},{"issue":"2","key":"1514_CR25","doi-asserted-by":"publisher","first-page":"R16","DOI":"10.1186\/gb-2005-6-2-r16","volume":"6","author":"SE Choe","year":"2005","unstructured":"Choe SE, Boutros M, Michelson AM, Church GM, Halfon MS: Preferred analysis methods for Affymetrix GeneChips revealed by a wholly defined control dataset. Genome Biol 2005, 6(2):R16. 10.1186\/gb-2005-6-2-r16","journal-title":"Genome Biol"},{"issue":"3","key":"1514_CR26","doi-asserted-by":"publisher","first-page":"323","DOI":"10.1093\/bioinformatics\/btg410","volume":"20","author":"LM Cope","year":"2004","unstructured":"Cope LM, Irizarry RA, Jaffee HA, Wu Z, Speed TP: A benchmark for Affymetrix GeneChip expression measures. Bioinformatics 2004, 20(3):323\u2013331. 10.1093\/bioinformatics\/btg410","journal-title":"Bioinformatics"},{"issue":"3","key":"1514_CR27","doi-asserted-by":"publisher","first-page":"401","DOI":"10.1186\/gb-2006-7-3-401","volume":"7","author":"AR Dabney","year":"2006","unstructured":"Dabney AR, Storey JD: A reanalysis of a published Affymetrix GeneChip control dataset. Genome Biol 2006, 7(3):401. 10.1186\/gb-2006-7-3-401","journal-title":"Genome Biol"},{"issue":"5","key":"1514_CR28","doi-asserted-by":"crossref","first-page":"434","DOI":"10.1055\/s-0038-1633893","volume":"43","author":"J Freudenberg","year":"2004","unstructured":"Freudenberg J, Boriss H, Hasenclever D: Comparison of preprocessing procedures for oligo-nucleotide micro-arrays by parametric bootstrap simulation of spike-in experiments. Methods Inf Med 2004, 43(5):434\u2013438.","journal-title":"Methods Inf Med"},{"issue":"4","key":"1514_CR29","doi-asserted-by":"publisher","first-page":"e15","DOI":"10.1093\/nar\/gng015","volume":"31","author":"RA Irizarry","year":"2003","unstructured":"Irizarry RA, Bolstad BM, Collin F, Cope LM, Hobbs B, Speed TP: Summaries of Affymetrix GeneChip probe level data. Nucleic Acids Res 2003, 31(4):e15. 10.1093\/nar\/gng015","journal-title":"Nucleic Acids Res"},{"issue":"2","key":"1514_CR30","doi-asserted-by":"publisher","first-page":"249","DOI":"10.1093\/biostatistics\/4.2.249","volume":"4","author":"RA Irizarry","year":"2003","unstructured":"Irizarry RA, Hobbs B, Collin F, Beazer-Barclay YD, Antonellis KJ, Scherf U, Speed TP: Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics 2003, 4(2):249\u2013264. 10.1093\/biostatistics\/4.2.249","journal-title":"Biostatistics"},{"key":"1514_CR31","unstructured":"Agilent: Agilent RNA Spike-In Kit Product Number 5188\u20135279. Agilent Technologies, Santa Clara, CA;"},{"key":"1514_CR32","first-page":"31","volume":"12","author":"I Lonnstedt","year":"2003","unstructured":"Lonnstedt I, Speed T: Replicated microarray data. Statistica Sinica 2003, 12: 31\u201346.","journal-title":"Statistica Sinica"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-8-142.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/article\/10.1186\/1471-2105-8-142\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-8-142.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,1,23]],"date-time":"2019-01-23T04:23:58Z","timestamp":1548217438000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/1471-2105-8-142"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2007,5,1]]},"references-count":32,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2007,12]]}},"alternative-id":["1514"],"URL":"https:\/\/doi.org\/10.1186\/1471-2105-8-142","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2007,5,1]]},"article-number":"142"}}