{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,8]],"date-time":"2026-01-08T07:11:21Z","timestamp":1767856281302,"version":"3.49.0"},"reference-count":21,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2010,6,24]],"date-time":"2010-06-24T00:00:00Z","timestamp":1277337600000},"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":[[2010,12]]},"DOI":"10.1186\/1471-2105-11-344","type":"journal-article","created":{"date-parts":[[2010,6,24]],"date-time":"2010-06-24T18:15:07Z","timestamp":1277403307000},"source":"Crossref","is-referenced-by-count":28,"title":["Error, reproducibility and sensitivity: a pipeline for data processing of Agilent oligonucleotide expression arrays"],"prefix":"10.1186","volume":"11","author":[{"given":"Benjamin","family":"Chain","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Helen","family":"Bowen","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"John","family":"Hammond","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Wilfried","family":"Posch","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jane","family":"Rasaiyaah","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jhen","family":"Tsang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mahdad","family":"Noursadeghi","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2010,6,24]]},"reference":[{"key":"3801_CR1","doi-asserted-by":"publisher","first-page":"1151","DOI":"10.1038\/nbt1239","volume":"24","author":"L Shi","year":"2006","unstructured":"Shi L, et al.: The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements. Nat Biotechnol 2006, 24: 1151\u20131161. 10.1038\/nbt1239","journal-title":"Nat Biotechnol"},{"key":"3801_CR2","unstructured":"Agilent Whole Human Genome Expression Arrays2010. [\n                    http:\/\/www.chem.agilent.com\/en-us\/products\/instruments\/dnamicroarrays\/wholehumangenomeoligomicroarraykit\/pages\/default.aspx\n                    \n                  ]"},{"key":"3801_CR3","doi-asserted-by":"publisher","first-page":"185","DOI":"10.1093\/bioinformatics\/19.2.185","volume":"19","author":"BM Bolstad","year":"2003","unstructured":"Bolstad BM, Irizarry RA, Astrand M, Speed TP: A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics 2003, 19: 185\u2013193. 10.1093\/bioinformatics\/19.2.185","journal-title":"Bioinformatics"},{"key":"3801_CR4","doi-asserted-by":"publisher","first-page":"242","DOI":"10.1093\/biostatistics\/kxp059","volume":"11","author":"MN McCall","year":"2010","unstructured":"McCall MN, Bolstad BM, Irizarry RA: Frozen robust multiarray analysis (fRMA). Biostatistics 2010, 11: 242\u2013253. 10.1093\/biostatistics\/kxp059","journal-title":"Biostatistics"},{"key":"3801_CR5","doi-asserted-by":"publisher","first-page":"93","DOI":"10.1002\/9781118887486","volume-title":"Applied multivariate data analysis","author":"BS Everitt","year":"2001","unstructured":"Everitt BS, Dunn J: Multidimensional scaling. In Applied multivariate data analysis. 2nd edition. Hodder Arnold, London, UK; 2001:93\u2013122.","edition":"2"},{"key":"3801_CR6","doi-asserted-by":"publisher","first-page":"429","DOI":"10.1111\/j.1365-2567.2008.03018.x","volume":"127","author":"J Rasaiyaah","year":"2009","unstructured":"Rasaiyaah J, Noursadeghi M, Kellam P, Chain B: Transcriptional and functional defects of dendritic cells derived from the MUTZ-3 leukaemia line. Immunology 2009, 127: 429\u2013441. 10.1111\/j.1365-2567.2008.03018.x","journal-title":"Immunology"},{"issue":"Suppl 1","key":"3801_CR7","doi-asserted-by":"publisher","first-page":"S105","DOI":"10.1093\/bioinformatics\/18.suppl_1.S105","volume":"18","author":"BP Durbin","year":"2002","unstructured":"Durbin BP, Hardin JS, Hawkins DM, Rocke DM: A variance-stabilizing transformation for gene-expression microarray data. Bioinformatics 2002, 18(Suppl 1):S105-S110.","journal-title":"Bioinformatics"},{"key":"3801_CR8","doi-asserted-by":"publisher","first-page":"e50","DOI":"10.1093\/nar\/30.11.e50","volume":"30","author":"TC Kroll","year":"2002","unstructured":"Kroll TC, Wolfl S: Ranking: a closer look on globalisation methods for normalisation of gene expression arrays. Nucleic Acids Res 2002, 30: e50. 10.1093\/nar\/30.11.e50","journal-title":"Nucleic Acids Res"},{"key":"3801_CR9","doi-asserted-by":"publisher","first-page":"R44","DOI":"10.1186\/gb-2007-8-3-r44","volume":"8","author":"AR Dabney","year":"2007","unstructured":"Dabney AR, Storey JD: Normalization of two-channel microarrays accounting for experimental design and intensity-dependent relationships. Genome Biol 2007, 8: R44. 10.1186\/gb-2007-8-3-r44","journal-title":"Genome Biol"},{"key":"3801_CR10","doi-asserted-by":"publisher","first-page":"128","DOI":"10.1093\/biostatistics\/kxj038","volume":"8","author":"AR Dabney","year":"2007","unstructured":"Dabney AR, Storey JD: A new approach to intensity-dependent normalization of two-channel microarrays. Biostatistics 2007, 8: 128\u2013139. 10.1093\/biostatistics\/kxj038","journal-title":"Biostatistics"},{"key":"3801_CR11","doi-asserted-by":"publisher","first-page":"2391","DOI":"10.1093\/bioinformatics\/btm361","volume":"23","author":"J Fan","year":"2007","unstructured":"Fan J, Niu Y: Selection and validation of normalization methods for c-DNA microarrays using within-array replications. Bioinformatics 2007, 23: 2391\u20132398. 10.1093\/bioinformatics\/btm361","journal-title":"Bioinformatics"},{"key":"3801_CR12","doi-asserted-by":"publisher","first-page":"415","DOI":"10.1080\/10543400701199544","volume":"17","author":"D Wang","year":"2007","unstructured":"Wang D, Zhang CH, Soares MB, Huang J: Systematic approaches for incorporating control spots and data quality information to improve normalization of cDNA microarray data. J Biopharm Stat 2007, 17: 415\u2013431. 10.1080\/10543400701199544","journal-title":"J Biopharm Stat"},{"key":"3801_CR13","doi-asserted-by":"publisher","first-page":"1140","DOI":"10.1038\/nbt1242","volume":"24","author":"TA Patterson","year":"2006","unstructured":"Patterson TA, Lobenhofer EK, Fulmer-Smentek SB, Collins PJ, Chu TM, Bao W, Fang H, Kawasaki ES, Hager J, Tikhonova IR, Walker SJ, Zhang L, Hurban P, de Longueville F, Fuscoe JC, Tong W, Shi L, Wolfinger RD: Performance comparison of one-color and two-color platforms within the MicroArray Quality Control (MAQC) project. Nat Biotechnol 2006, 24: 1140\u20131150. 10.1038\/nbt1242","journal-title":"Nat Biotechnol"},{"key":"3801_CR14","doi-asserted-by":"publisher","first-page":"118","DOI":"10.1093\/biostatistics\/kxj037","volume":"8","author":"WE Johnson","year":"2007","unstructured":"Johnson WE, Li C, Rabinovic A: Adjusting batch effects in microarray expression data using empirical Bayes methods. Biostatistics 2007, 8: 118\u2013127. 10.1093\/biostatistics\/kxj037","journal-title":"Biostatistics"},{"key":"3801_CR15","doi-asserted-by":"publisher","first-page":"956","DOI":"10.1126\/science.1160342","volume":"321","author":"M Sultan","year":"2008","unstructured":"Sultan M, Schulz MH, Richard H, Magen A, Klingenhoff A, Scherf M, Seifert M, Borodina T, Soldatov A, Parkhomchuk D, Schmidt D, O'Keeffe S, Haas S, Vingron M, Lehrach H, Yaspo ML: A global view of gene activity and alternative splicing by deep sequencing of the human transcriptome. Science 2008, 321: 956\u2013960. 10.1126\/science.1160342","journal-title":"Science"},{"key":"3801_CR16","doi-asserted-by":"publisher","first-page":"e141","DOI":"10.1093\/nar\/gkn705","volume":"36","author":"PA 't Hoen","year":"2008","unstructured":"'t Hoen PA, Ariyurek Y, Thygesen HH, Vreugdenhil E, Vossen RH, de Menezes RX, Boer JM, van Ommen GJ, den Dunnen JT: Deep sequencing-based expression analysis shows major advances in robustness, resolution and inter-lab portability over five microarray platforms. Nucleic Acids Res 2008, 36: e141. 10.1093\/nar\/gkn705","journal-title":"Nucleic Acids Res"},{"key":"3801_CR17","doi-asserted-by":"publisher","first-page":"799","DOI":"10.1038\/nature05874","volume":"447","author":"E Birney","year":"2007","unstructured":"Birney E, et al.: Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 2007, 447: 799\u2013816. 10.1038\/nature05874","journal-title":"Nature"},{"key":"3801_CR18","doi-asserted-by":"publisher","first-page":"319","DOI":"10.4049\/jimmunol.182.1.319","volume":"182","author":"M Noursadeghi","year":"2009","unstructured":"Noursadeghi M, Tsang J, Miller RF, Straschewski S, Kellam P, Chain BM, Katz DR: Genome-wide innate immune responses in HIV-1-infected macrophages are preserved despite attenuation of the NF-kappa B activation pathway. J Immunol 2009, 182: 319\u2013328.","journal-title":"J Immunol"},{"key":"3801_CR19","doi-asserted-by":"publisher","first-page":"429","DOI":"10.1111\/j.1365-2567.2008.03018.x","volume":"127","author":"J Rasaiyaah","year":"2009","unstructured":"Rasaiyaah J, Noursadeghi M, Kellam P, Chain B: Transcriptional and functional defects of dendritic cells derived from the MUTZ-3 leukaemia line. Immunology 2009, 127: 429\u2013441. 10.1111\/j.1365-2567.2008.03018.x","journal-title":"Immunology"},{"key":"3801_CR20","doi-asserted-by":"publisher","first-page":"3824","DOI":"10.1104\/pp.104.046672","volume":"136","author":"CR Hampton","year":"2004","unstructured":"Hampton CR, Bowen HC, Broadley MR, Hammond JP, Mead A, Payne KA, Pritchard J, White PJ: Cesium toxicity in Arabidopsis. Plant Physiol 2004, 136: 3824\u20133837. 10.1104\/pp.104.046672","journal-title":"Plant Physiol"},{"key":"3801_CR21","doi-asserted-by":"publisher","first-page":"239","DOI":"10.1111\/j.1469-8137.2006.01662.x","volume":"170","author":"JP Hammond","year":"2006","unstructured":"Hammond JP, Bowen HC, White PJ, Mills V, Pyke KA, Baker AJ, Whiting SN, May ST, Broadley MR: A comparison of the Thlaspi caerulescens and Thlaspi arvense shoot transcriptomes. New Phytol 2006, 170: 239\u2013260. 10.1111\/j.1469-8137.2006.01662.x","journal-title":"New Phytol"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-11-344.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/article\/10.1186\/1471-2105-11-344\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-11-344.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,1,22]],"date-time":"2019-01-22T13:21:19Z","timestamp":1548163279000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/1471-2105-11-344"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2010,6,24]]},"references-count":21,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2010,12]]}},"alternative-id":["3801"],"URL":"https:\/\/doi.org\/10.1186\/1471-2105-11-344","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2010,6,24]]},"article-number":"344"}}