{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,28]],"date-time":"2026-07-28T05:15:50Z","timestamp":1785215750103,"version":"3.55.0"},"reference-count":5,"publisher":"Oxford University Press (OUP)","issue":"13","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2008,7,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: Illumina microarray is becoming a popular microarray platform. The BeadArray technology from Illumina makes its preprocessing and quality control different from other microarray technologies. Unfortunately, most other analyses have not taken advantage of the unique properties of the BeadArray system, and have just incorporated preprocessing methods originally designed for Affymetrix microarrays. lumi is a Bioconductor package especially designed to process the Illumina microarray data. It includes data input, quality control, variance stabilization, normalization and gene annotation portions. In specific, the lumi package includes a variance-stabilizing transformation (VST) algorithm that takes advantage of the technical replicates available on every Illumina microarray. Different normalization method options and multiple quality control plots are provided in the package. To better annotate the Illumina data, a vendor independent nucleotide universal identifier (nuID) was devised to identify the probes of Illumina microarray. The nuID annotation packages and output of lumi processed results can be easily integrated with other Bioconductor packages to construct a statistical data analysis pipeline for Illumina data.<\/jats:p>\n               <jats:p>Availability: The lumi Bioconductor package, www.bioconductor.org<\/jats:p>\n               <jats:p>Contact: \u00a0dupan@northwestern.edu<\/jats:p>","DOI":"10.1093\/bioinformatics\/btn224","type":"journal-article","created":{"date-parts":[[2008,5,9]],"date-time":"2008-05-09T00:34:00Z","timestamp":1210293240000},"page":"1547-1548","source":"Crossref","is-referenced-by-count":1873,"title":["<i>lumi<\/i>: a pipeline for processing Illumina microarray"],"prefix":"10.1093","volume":"24","author":[{"given":"Pan","family":"Du","sequence":"first","affiliation":[{"name":"Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL, 60611, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Warren A.","family":"Kibbe","sequence":"additional","affiliation":[{"name":"Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL, 60611, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Simon M.","family":"Lin","sequence":"additional","affiliation":[{"name":"Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL, 60611, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2008,5,8]]},"reference":[{"key":"2023020210370018700_B1","doi-asserted-by":"crossref","first-page":"16","DOI":"10.1186\/1745-6150-2-16","article-title":"nuID: a universal naming scheme of oligonucleotides for Illumina, Affymetrix, and other microarrays","volume":"2","author":"Du","year":"2007","journal-title":"Biol. Direct"},{"key":"2023020210370018700_B2","doi-asserted-by":"crossref","first-page":"2183","DOI":"10.1093\/bioinformatics\/btm311","article-title":"beadarray: R classes and methods for Illumina bead-based data","volume":"23","author":"Dunning","year":"2007","journal-title":"Bioinformatics"},{"key":"2023020210370018700_B3","doi-asserted-by":"crossref","first-page":"R80","DOI":"10.1186\/gb-2004-5-10-r80","article-title":"Bioconductor: open software development for computational biology and bioinformatics","volume":"5","author":"Gentleman","year":"2004","journal-title":"Genome Biol"},{"key":"2023020210370018700_B4","doi-asserted-by":"crossref","first-page":"2347","DOI":"10.1101\/gr.2739104","article-title":"A novel, high-performance random array platform for quantitative gene expression profiling","volume":"14","author":"Kuhn","year":"2004","journal-title":"Genome Res"},{"key":"2023020210370018700_B5","doi-asserted-by":"crossref","first-page":"e11","DOI":"10.1093\/nar\/gkm1075","article-title":"Model-based variance-stabilizing transformation for Illumina microarray data","volume":"36","author":"Lin","year":"2008","journal-title":"Nucleic Acid Res"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/24\/13\/1547\/49052190\/bioinformatics_24_13_1547.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/24\/13\/1547\/49052190\/bioinformatics_24_13_1547.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,2,2]],"date-time":"2023-02-02T10:41:28Z","timestamp":1675334488000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/24\/13\/1547\/238285"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2008,5,8]]},"references-count":5,"journal-issue":{"issue":"13","published-print":{"date-parts":[[2008,7,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btn224","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2008,7,1]]},"published":{"date-parts":[[2008,5,8]]}}}