{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,12]],"date-time":"2026-03-12T04:21:09Z","timestamp":1773289269828,"version":"3.50.1"},"reference-count":32,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2004,10,25]],"date-time":"2004-10-25T00:00:00Z","timestamp":1098662400000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/2.0"},{"start":{"date-parts":[[2004,10,25]],"date-time":"2004-10-25T00:00:00Z","timestamp":1098662400000},"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>One of the important challenges in microarray analysis is to take full advantage of previously accumulated data, both from one's own laboratory and from public repositories. Through a comparative analysis on a variety of datasets, a more comprehensive view of the underlying mechanism or structure can be obtained. However, as we discover in this work, continual changes in genomic sequence annotations and probe design criteria make it difficult to compare gene expression data even from different generations of the same microarray platform.<\/jats:p>\n                     <\/jats:sec><jats:sec>\n                        <jats:title>Results<\/jats:title>\n                        <jats:p>We first describe the extent of discordance between the results derived from two generations of Affymetrix oligonucleotide arrays, as revealed in cluster analysis and in identification of differentially expressed genes. We then propose a method for increasing comparability. The dataset we use consists of a set of 14 human muscle biopsy samples from patients with inflammatory myopathies that were hybridized on both HG-U95Av2 and HG-U133A human arrays. We find that the use of the probe set matching table for comparative analysis provided by Affymetrix produces better results than matching by UniGene or LocusLink identifiers but still remains inadequate. Rescaling of expression values for each gene across samples and data filtering by expression values enhance comparability but only for few specific analyses. As a generic method for improving comparability, we select a subset of probes with overlapping sequence segments in the two array types and recalculate expression values based only on the selected probes. We show that this filtering of probes significantly improves the comparability while retaining a sufficient number of probe sets for further analysis.<\/jats:p>\n                     <\/jats:sec><jats:sec>\n                        <jats:title>Conclusions<\/jats:title>\n                        <jats:p>Compatibility between high-density oligonucleotide arrays is significantly affected by probe-level sequence information. With a careful filtering of the probes based on their sequence overlaps, data from different generations of microarrays can be combined more effectively.<\/jats:p>\n                     <\/jats:sec>","DOI":"10.1186\/1471-2105-5-159","type":"journal-article","created":{"date-parts":[[2004,10,29]],"date-time":"2004-10-29T13:25:43Z","timestamp":1099056343000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":40,"title":["Combining gene expression data from different generations of oligonucleotide arrays"],"prefix":"10.1186","volume":"5","author":[{"given":"Kyu-Baek","family":"Hwang","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sek Won","family":"Kong","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Steve A","family":"Greenberg","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Peter J","family":"Park","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2004,10,25]]},"reference":[{"issue":"3","key":"275_CR1","doi-asserted-by":"publisher","first-page":"236","DOI":"10.1038\/73439","volume":"24","author":"U Scherf","year":"2000","unstructured":"Scherf U, Ross DT, Waltham M, Smith LH, Lee JK, Tanabe L, Kohn KW, Reinhold WC, Myers TG, Andrews DT, Scudiero DA, Eisen MB, Sausville EA, Pommier Y, Botstein D, Brown PO, Weinstein JN: A gene expression database for the molecular pharmacology of cancer.\n                           Nat Genet 2000, 24(3):236\u2013244. 10.1038\/73439","journal-title":"Nat Genet"},{"issue":"8","key":"275_CR2","doi-asserted-by":"publisher","first-page":"539","DOI":"10.1056\/NEJM200102223440801","volume":"344","author":"I Hedenfalk","year":"2001","unstructured":"Hedenfalk I, Duggan D, Chen Y, Radmacher M, Bittner M, Simon R, Meltzer P, Gusterson B, Esteller M, Raffeld M, Yakhini Z, Ben-Dor A, Dougherty E, Kononen J, Bubendorf L, Fehrle W, Pittaluga S, Gruvberger S, Loman N, Johannsson O, Olsson H, Wilfond B, Sauter G, Kallioniemi OP, Borg A, Trent J: Gene-Expression Profiles in Hereditary Breast Cancer.\n                           N Engl J Med 2001, 344(8):539\u2013548. 10.1056\/NEJM200102223440801","journal-title":"N Engl J Med"},{"issue":"6871","key":"275_CR3","doi-asserted-by":"publisher","first-page":"530","DOI":"10.1038\/415530a","volume":"415","author":"LJ van't Veer","year":"2002","unstructured":"van't Veer LJ, Dai H, van de Vijver MJ, He YD, Hart AAM, Mao M, Peterse HL, van der Kooy K, Marton MJ, Witteveen AT, Schreiber GJ, Kerkhoven RM, Roberts C, Linsley PS, Bernards R, Friend SH: Gene expression profiling predicts clinical outcome of breast cancer.\n                           Nature 2002, 415(6871):530\u2013536. 10.1038\/415530a","journal-title":"Nature"},{"key":"275_CR4","volume-title":"The Analysis of Gene Expression Data","year":"2003","unstructured":"Parmigiani G, Garrett E, Irizarry R, Zeger S, (Eds): The Analysis of Gene Expression Data. 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