{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,20]],"date-time":"2026-05-20T13:01:09Z","timestamp":1779282069540,"version":"3.51.4"},"reference-count":12,"publisher":"Oxford University Press (OUP)","issue":"24","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":2899,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/2.0\/uk\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2008,12,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: With their many replicates and their random layouts, Illumina BeadArrays provide greater scope fordetecting spatial artefacts than do other microarray technologies. They are also robust to artefact exclusion, yet there is a lack of tools that can perform these tasks for Illumina. We present BASH, a tool for this purpose. BASH adopts the concepts of Harshlight, but implements them in a manner that utilizes the unique characteristics of the Illumina technology. Using bead-level data, spatial artefacts of various kinds can thus be identified and excluded from further analyses.<\/jats:p>\n               <jats:p>Availability: The beadarray Bioconductor package (version 1.10 onwards), www.bioconductor.org<\/jats:p>\n               <jats:p>Contact: \u00a0andy.lynch@cancer.org.uk<\/jats:p>\n               <jats:p>Supplementary information: Additional information and a vignette are included in the beadarray package.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btn557","type":"journal-article","created":{"date-parts":[[2008,10,26]],"date-time":"2008-10-26T00:14:13Z","timestamp":1224980053000},"page":"2921-2922","source":"Crossref","is-referenced-by-count":55,"title":["BASH: a tool for managing BeadArray spatial artefacts"],"prefix":"10.1093","volume":"24","author":[{"given":"J. M.","family":"Cairns","sequence":"first","affiliation":[{"name":"Cancer Research UK, Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"M. J.","family":"Dunning","sequence":"additional","affiliation":[{"name":"Cancer Research UK, Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"M. E.","family":"Ritchie","sequence":"additional","affiliation":[{"name":"Cancer Research UK, Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"R.","family":"Russell","sequence":"additional","affiliation":[{"name":"Cancer Research UK, Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"A. G.","family":"Lynch","sequence":"additional","affiliation":[{"name":"Cancer Research UK, Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2008,10,25]]},"reference":[{"key":"2023020212295725400_B1","first-page":"1","article-title":"Quality control and low-level statistical analysis of Illumina BeadArrays","volume":"4","author":"Dunning","year":"2006","journal-title":"REVSTAT"},{"key":"2023020212295725400_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":"2023020212295725400_B3","doi-asserted-by":"crossref","first-page":"85","DOI":"10.1186\/1471-2105-9-85","article-title":"Statistical issues in the analysis of Illumina data","volume":"9","author":"Dunning","year":"2008","journal-title":"BMC Bioinformatics"},{"key":"2023020212295725400_B4","doi-asserted-by":"crossref","first-page":"31","DOI":"10.1073\/pnas.98.1.31","article-title":"Model-based analysis of oligonucleotide arrays: expression index computation and outlier detection","volume":"98","author":"Li","year":"2001","journal-title":"Proc. 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