{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,27]],"date-time":"2025-10-27T04:57:08Z","timestamp":1761541028468},"reference-count":21,"publisher":"Oxford University Press (OUP)","issue":"5","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2011,3,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Bead arrays are becoming a popular platform for high-throughput expression arrays. However, the number of the beads targeting a transcript and the variation of their intensities differ from sample to sample in these arrays. This property results in different accuracy of expression intensities of a transcript across arrays.<\/jats:p>\n               <jats:p>Results: We provide evidence, with publicly available spike-in data, that the false discovery rate of differential expression is reduced by modeling bead-level variability with a multi-level mixed effects model. We compare the performance of our proposed model to existing analysis methods for bead arrays: the unweighted t-test and other weighted methods. Additionally, we provide theoretical insights into when the multi-level mixed effects model outperforms other methods. Finally, we provide a software program for differential expression analysis using the multi-level mixed effects model that analyzes tens of thousands of genes efficiently.<\/jats:p>\n               <jats:p>Availability: The software program is freely available on web at http:\/\/ephpublic.aecom.yu.edu\/sites\/rkim\/Supplementary.<\/jats:p>\n               <jats:p>Contact: \u00a0ryung.kim@einstein.yu.edu<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btq708","type":"journal-article","created":{"date-parts":[[2010,12,18]],"date-time":"2010-12-18T03:20:38Z","timestamp":1292642438000},"page":"633-640","source":"Crossref","is-referenced-by-count":2,"title":["Multi-level mixed effects models for bead arrays"],"prefix":"10.1093","volume":"27","author":[{"given":"Ryung S.","family":"Kim","sequence":"first","affiliation":[{"name":"Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY 10461, USA"}]},{"given":"Juan","family":"Lin","sequence":"additional","affiliation":[{"name":"Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY 10461, USA"}]}],"member":"286","published-online":{"date-parts":[[2010,12,17]]},"reference":[{"key":"2023012511573354000_B1","doi-asserted-by":"crossref","first-page":"1438","DOI":"10.1093\/hmg\/ddq018","article-title":"Transcriptional changes in Huntington disease identified using genome-wide expression profiling and cross-platform analysis","volume":"19","author":"Becanovic","year":"2010","journal-title":"Hum. 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