{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,9]],"date-time":"2026-01-09T12:27:39Z","timestamp":1767961659223,"version":"3.49.0"},"reference-count":29,"publisher":"Oxford University Press (OUP)","issue":"7","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2011,4,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Titration experiments measuring the gene expression from two different tissues, along with total RNA mixtures of the pure samples, are frequently used for quality evaluation of microarray technologies. Such a design implies that the true mRNA expression of each gene, is either constant or follows a monotonic trend between the mixtures, applying itself to the use of order restricted inference procedures. Exploiting only the postulated monotonicity of titration designs, we propose three statistical analysis methods for the validation of high-throughput genetic data and corresponding preprocessing techniques.<\/jats:p>\n               <jats:p>Results: Our methods allow for inference of accuracy, repeatability and cross-platform agreement, with minimal required assumptions regarding the underlying data generating process. Therefore, they are readily applicable to all sorts of genetic high-throughput data independent of the degree of preprocessing. An application to the EMERALD dataset was used to demonstrate how our methods provide a rich spectrum of easily interpretable quality metrics and allow the comparison of different microarray technologies and normalization methods. The results are on par with previous work, but provide additional new insights that cast doubt on the utility of popular preprocessing techniques, specifically concerning the EMERALD projects dataset.<\/jats:p>\n               <jats:p>Availability: All datasets are available on EBI's ArrayExpress web site http:\/\/www.ebi.ac.uk\/microarray-as\/ae\/) under accession numbers E-TABM-536, E-TABM-554 and E-TABM-555. Source code implemented in C and R is available at: http:\/\/statistics.msi.meduniwien.ac.at\/float\/cross_platform\/.<\/jats:p>\n               <jats:p>Methods for testing and variance decomposition have been made available in the R-package orQA, which can be downloaded and installed from CRAN http:\/\/cran.r-project.org.<\/jats:p>\n               <jats:p>Contact: \u00a0martin.posch.mail@gmail.com<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btr066","type":"journal-article","created":{"date-parts":[[2011,2,12]],"date-time":"2011-02-12T01:30:50Z","timestamp":1297474250000},"page":"953-960","source":"Crossref","is-referenced-by-count":8,"title":["Cross-platform comparison of microarray data using order restricted inference"],"prefix":"10.1093","volume":"27","author":[{"given":"Florian","family":"Klinglmueller","sequence":"first","affiliation":[{"name":"1 Center for Medical Statistics, Informatics and Intelligent Systems, Medical University of Vienna, Spitalgasse 23, A-1090 Vienna and 2Department of Biotechnology, University for Life Sciences and Natural Resources, Muthgasse 18, 1190 Vienna, Austria"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Thomas","family":"Tuechler","sequence":"additional","affiliation":[{"name":"1 Center for Medical Statistics, Informatics and Intelligent Systems, Medical University of Vienna, Spitalgasse 23, A-1090 Vienna and 2Department of Biotechnology, University for Life Sciences and Natural Resources, Muthgasse 18, 1190 Vienna, Austria"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Martin","family":"Posch","sequence":"additional","affiliation":[{"name":"1 Center for Medical Statistics, Informatics and Intelligent Systems, Medical University of Vienna, Spitalgasse 23, A-1090 Vienna and 2Department of Biotechnology, University for Life Sciences and Natural Resources, Muthgasse 18, 1190 Vienna, Austria"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2011,2,10]]},"reference":[{"key":"2023012512175840500_B1","volume-title":"Statistical Inference Under Order Restrictions.","author":"Barlow","year":"1972"},{"key":"2023012512175840500_B2","doi-asserted-by":"crossref","first-page":"5914","DOI":"10.1093\/nar\/gki890","article-title":"Experimental comparison and cross-validation of the Affymetrix and Illumina gene expression analysis platforms","volume":"33","author":"Barnes","year":"2005","journal-title":"Nucleic Acids Res."},{"key":"2023012512175840500_B3","doi-asserted-by":"crossref","first-page":"607","DOI":"10.1214\/aoms\/1177728420","article-title":"Maximum likelihood estimates of monotone parameters","volume":"26","author":"Brunk","year":"1955","journal-title":"Ann. 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