{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,6]],"date-time":"2026-01-06T05:13:28Z","timestamp":1767676408500,"version":"build-2065373602"},"reference-count":31,"publisher":"Springer Science and Business Media LLC","issue":"S2","license":[{"start":{"date-parts":[[2005,7,1]],"date-time":"2005-07-01T00:00:00Z","timestamp":1120176000000},"content-version":"tdm","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"],"published-print":{"date-parts":[[2005,7]]},"abstract":"<jats:title>Abstract<\/jats:title>\n          <jats:sec>\n            <jats:title>Background<\/jats:title>\n            <jats:p>The acceptance of microarray technology in regulatory decision-making is being challenged by the existence of various platforms and data analysis methods. A recent report (E. Marshall, <jats:italic>Science<\/jats:italic>, 306, 630\u2013631, 2004), by extensively citing the study of Tan <jats:italic>et al<\/jats:italic>. (<jats:italic>Nucleic Acids Res<\/jats:italic>., 31, 5676\u20135684, 2003), portrays a disturbingly negative picture of the cross-platform comparability, and, hence, the reliability of microarray technology.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Results<\/jats:title>\n            <jats:p>We reanalyzed Tan's dataset and found that the intra-platform consistency was low, indicating a problem in experimental procedures from which the dataset was generated. Furthermore, by using three gene selection methods (<jats:italic>i.e.<\/jats:italic>, <jats:italic>p<\/jats:italic>-value ranking, fold-change ranking, and Significance Analysis of Microarrays (SAM)) on the same dataset we found that <jats:italic>p<\/jats:italic>-value ranking (the method emphasized by Tan <jats:italic>et al<\/jats:italic>.) results in much lower cross-platform concordance compared to fold-change ranking or SAM. Therefore, the low cross-platform concordance reported in Tan's study appears to be mainly due to a combination of low intra-platform consistency and a poor choice of data analysis procedures, instead of inherent technical differences among different platforms, as suggested by Tan <jats:italic>et al<\/jats:italic>. and Marshall.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Conclusion<\/jats:title>\n            <jats:p>Our results illustrate the importance of establishing calibrated RNA samples and reference datasets to objectively assess the performance of different microarray platforms and the proficiency of individual laboratories as well as the merits of various data analysis procedures. Thus, we are progressively coordinating the MAQC project, a community-wide effort for microarray quality control.<\/jats:p>\n          <\/jats:sec>","DOI":"10.1186\/1471-2105-6-s2-s12","type":"journal-article","created":{"date-parts":[[2005,7,16]],"date-time":"2005-07-16T09:00:41Z","timestamp":1121504441000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":139,"title":["Cross-platform comparability of microarray technology: Intra-platform consistency and appropriate data analysis procedures are essential"],"prefix":"10.1186","volume":"6","author":[{"given":"Leming","family":"Shi","sequence":"first","affiliation":[]},{"given":"Weida","family":"Tong","sequence":"additional","affiliation":[]},{"given":"Hong","family":"Fang","sequence":"additional","affiliation":[]},{"given":"Uwe","family":"Scherf","sequence":"additional","affiliation":[]},{"given":"Jing","family":"Han","sequence":"additional","affiliation":[]},{"given":"Raj K","family":"Puri","sequence":"additional","affiliation":[]},{"given":"Felix W","family":"Frueh","sequence":"additional","affiliation":[]},{"given":"Federico M","family":"Goodsaid","sequence":"additional","affiliation":[]},{"given":"Lei","family":"Guo","sequence":"additional","affiliation":[]},{"given":"Zhenqiang","family":"Su","sequence":"additional","affiliation":[]},{"given":"Tao","family":"Han","sequence":"additional","affiliation":[]},{"given":"James C","family":"Fuscoe","sequence":"additional","affiliation":[]},{"given":"Z aAlex","family":"Xu","sequence":"additional","affiliation":[]},{"given":"Tucker A","family":"Patterson","sequence":"additional","affiliation":[]},{"given":"Huixiao","family":"Hong","sequence":"additional","affiliation":[]},{"given":"Qian","family":"Xie","sequence":"additional","affiliation":[]},{"given":"Roger G","family":"Perkins","sequence":"additional","affiliation":[]},{"given":"James J","family":"Chen","sequence":"additional","affiliation":[]},{"given":"Daniel A","family":"Casciano","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2005,7,15]]},"reference":[{"issue":"Suppl","key":"670_CR1","doi-asserted-by":"publisher","first-page":"474","DOI":"10.1038\/ng1029","volume":"32","author":"EF Petricoin 3rd","year":"2002","unstructured":"Petricoin EF 3rd, Hackett JL, Lesko LJ, Puri RK, Gutman SI, Chumakov K, Woodcock J, Feigal DW Jr, Zoon KC, Sistare FD: Medical applications of microarray technologies: a regulatory science perspective. 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