A new normalizing algorithm for BAC CGH arrays with quality control metrics.
The main focus in pin-tip (or print-tip) microarray analysis is determining which probes, genes, or oligonucleotides are differentially expressed. Specifically in array comparative genomic hybridization (aCGH) experiments, researchers search for chromosomal imbalances in the genome. To model this da...
| Published in: | Journal of Biomedicine & Biotechnology pp. 860732 - 860733 |
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| Main Authors: | , , , , |
| Format: | research Journal Article |
| Published: |
Wiley-Blackwell
2011
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| Online Access: | View this record in EBSCOhost |
| fields | @attributes: recordID: 1 pdfLink: plink: https://search.ebscohost.com/login.aspx?direct=true&db=ccm&AN=104531578&site=ehost-live header: @attributes: shortDbName: ccm uiTerm: 104531578 longDbName: CINAHL Complete uiTag: AN controlInfo: bkinfo: dissinfo: jinfo: jid: 11107243 137K jtl: Journal of Biomedicine & Biotechnology issn: 11107243 maglogo: N pubinfo: dt: 2011 pid: 480 pub: Wiley-Blackwell place: Malden, Massachusetts artinfo: ui: 104531578 104531578 2011456989 NLM21403910 PMC3043322 104531578 ppf: 860732 ppct: 1 formats: fmt: @attributes: type: P tig: atl: A new normalizing algorithm for BAC CGH arrays with quality control metrics. aug: au: Miecznikowski, Jeffrey C Gaile, Daniel P Liu, Song Shepherd, Lori Nowak, Norma affil: Department of Biostatistics, University at Buffalo, Buffalo, NY 14214, USA. jcm38@buffalo.edu sug: subj: Algorithms Cytogenetic Analysis Standards Quality Control (Technology) Chromosome Mapping Methods Chromosomes Cytogenetic Analysis Statistics and Numerical Data DNA Probes Data Analysis, Statistical Genome, Human Software ab: The main focus in pin-tip (or print-tip) microarray analysis is determining which probes, genes, or oligonucleotides are differentially expressed. Specifically in array comparative genomic hybridization (aCGH) experiments, researchers search for chromosomal imbalances in the genome. To model this data, scientists apply statistical methods to the structure of the experiment and assume that the data consist of the signal plus random noise. In this paper we propose 'SmoothArray', a new method to preprocess comparative genomic hybridization (CGH) bacterial artificial chromosome (BAC) arrays and we show the effects on a cancer dataset. As part of our R software package 'aCGHplus,' this freely available algorithm removes the variation due to the intensity effects, pin/print-tip, the spatial location on the microarray chip, and the relative location from the well plate. removal of this variation improves the downstream analysis and subsequent inferences made on the data. Further, we present measures to evaluate the quality of the dataset according to the arrayer pins, 384-well plates, plate rows, and plate columns. We compare our method against competing methods using several metrics to measure the biological signal. With this novel normalization algorithm and quality control measures, the user can improve their inferences on datasets and pinpoint problems that may arise in their BAC aCGH technology. pubtype: Academic Journal doctype: research Journal Article ougenre: Article language: English refInfo: holdings: @attributes: islocal: N |
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