{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,6]],"date-time":"2026-05-06T08:40:50Z","timestamp":1778056850232,"version":"3.51.4"},"reference-count":33,"publisher":"Oxford University Press (OUP)","issue":"9","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2011,5,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Spike-in datasets provide a valuable resource for assessing and comparing among competing microarray analysis strategies. Our previous wholly defined spike-in datasets, the Golden and Platinum Spikes, have provided insights for the analysis of Affymetrix GeneChips. However, a similar dataset, in which all cRNA identities and relative levels are known prospectively, has not been available for two-color platforms.<\/jats:p>\n               <jats:p>Results: We have generated a wholly defined spike-in dataset for Agilent microarrays consisting of 12 arrays with more than 2000 differentially expressed, and approximately 3600 background, cRNAs. The composition of this \u2018Ag Spike\u2019 dataset is identical to that of our previous Platinum Spike dataset and therefore allows direct cross-platform comparison. We demonstrate here the utility of the Ag Spike dataset for evaluating different analysis methods designed for two-color arrays. Comparison between the Ag Spike and Platinum Spike studies shows high agreement between results obtained using the Affymetrix and Agilent platforms.<\/jats:p>\n               <jats:p>Availability: The Ag Spike raw data can be accessed at http:\/\/www.ccr.buffalo.edu\/halfon\/spike\/index.html and through NCBI's Gene Expression Omnibus (GEO; accession GSE24866).<\/jats:p>\n               <jats:p>Contact: \u00a0qzhu@buffalo.edu; mshalfon@buffalo.edu.<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btr135","type":"journal-article","created":{"date-parts":[[2011,3,18]],"date-time":"2011-03-18T01:09:30Z","timestamp":1300410570000},"page":"1284-1289","source":"Crossref","is-referenced-by-count":7,"title":["A wholly defined Agilent microarray spike-in dataset"],"prefix":"10.1093","volume":"27","author":[{"given":"Qianqian","family":"Zhu","sequence":"first","affiliation":[{"name":"1 Department of Biochemistry, 2Department of Biostatistics, State University of New York at Buffalo, Buffalo, NY 14214, 3Department of Biostatistics, Roswell Park Cancer Institute, Buffalo, NY 14263, 4New York State Center of Excellence in Bioinformatics and Life Sciences, Buffalo, NY 14203, 5Department of Biological Sciences, State University of New York at Buffalo, Buffalo, NY 14260 and 6Department of Molecular and Cellular Biology, Roswell Park Cancer Institute, Buffalo, NY 14263, USA"},{"name":"1 Department of Biochemistry, 2Department of Biostatistics, State University of New York at Buffalo, Buffalo, NY 14214, 3Department of Biostatistics, Roswell Park Cancer Institute, Buffalo, NY 14263, 4New York State Center of Excellence in Bioinformatics and Life Sciences, Buffalo, NY 14203, 5Department of Biological Sciences, State University of New York at Buffalo, Buffalo, NY 14260 and 6Department of Molecular and Cellular Biology, Roswell Park Cancer Institute, Buffalo, NY 14263, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jeffrey C.","family":"Miecznikowski","sequence":"additional","affiliation":[{"name":"1 Department of Biochemistry, 2Department of Biostatistics, State University of New York at Buffalo, Buffalo, NY 14214, 3Department of Biostatistics, Roswell Park Cancer Institute, Buffalo, NY 14263, 4New York State Center of Excellence in Bioinformatics and Life Sciences, Buffalo, NY 14203, 5Department of Biological Sciences, State University of New York at Buffalo, Buffalo, NY 14260 and 6Department of Molecular and Cellular Biology, Roswell Park Cancer Institute, Buffalo, NY 14263, USA"},{"name":"1 Department of Biochemistry, 2Department of Biostatistics, State University of New York at Buffalo, Buffalo, NY 14214, 3Department of Biostatistics, Roswell Park Cancer Institute, Buffalo, NY 14263, 4New York State Center of Excellence in Bioinformatics and Life Sciences, Buffalo, NY 14203, 5Department of Biological Sciences, State University of New York at Buffalo, Buffalo, NY 14260 and 6Department of Molecular and Cellular Biology, Roswell Park Cancer Institute, Buffalo, NY 14263, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Marc S.","family":"Halfon","sequence":"additional","affiliation":[{"name":"1 Department of Biochemistry, 2Department of Biostatistics, State University of New York at Buffalo, Buffalo, NY 14214, 3Department of Biostatistics, Roswell Park Cancer Institute, Buffalo, NY 14263, 4New York State Center of Excellence in Bioinformatics and Life Sciences, Buffalo, NY 14203, 5Department of Biological Sciences, State University of New York at Buffalo, Buffalo, NY 14260 and 6Department of Molecular and Cellular Biology, Roswell Park Cancer Institute, Buffalo, NY 14263, USA"},{"name":"1 Department of Biochemistry, 2Department of Biostatistics, State University of New York at Buffalo, Buffalo, NY 14214, 3Department of Biostatistics, Roswell Park Cancer Institute, Buffalo, NY 14263, 4New York State Center of Excellence in Bioinformatics and Life Sciences, Buffalo, NY 14203, 5Department of Biological Sciences, State University of New York at Buffalo, Buffalo, NY 14260 and 6Department of Molecular and Cellular Biology, Roswell Park Cancer Institute, Buffalo, NY 14263, USA"},{"name":"1 Department of Biochemistry, 2Department of Biostatistics, State University of New York at Buffalo, Buffalo, NY 14214, 3Department of Biostatistics, Roswell Park Cancer Institute, Buffalo, NY 14263, 4New York State Center of Excellence in Bioinformatics and Life Sciences, Buffalo, NY 14203, 5Department of Biological Sciences, State University of New York at Buffalo, Buffalo, NY 14260 and 6Department of Molecular and Cellular Biology, Roswell Park Cancer Institute, Buffalo, NY 14263, USA"},{"name":"1 Department of Biochemistry, 2Department of Biostatistics, State University of New York at Buffalo, Buffalo, NY 14214, 3Department of Biostatistics, Roswell Park Cancer Institute, Buffalo, NY 14263, 4New York State Center of Excellence in Bioinformatics and Life Sciences, Buffalo, NY 14203, 5Department of Biological Sciences, State University of New York at Buffalo, Buffalo, NY 14260 and 6Department of Molecular and Cellular Biology, Roswell Park Cancer Institute, Buffalo, NY 14263, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2011,3,16]]},"reference":[{"key":"2023012512185362800_B1","doi-asserted-by":"crossref","first-page":"403","DOI":"10.1016\/S0022-2836(05)80360-2","article-title":"Basic local alignment search tool","volume":"215","author":"Altschul","year":"1990","journal-title":"J. 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