Title: Automatic quality assessment of Affymetrix GeneChip data
Authors : Heber, Steffen
Sick, Beate
Proceedings: Proceedings of the 44th annual Southeast regional conference
Pages : 411
Conference details: 44th ACM Southeast regional conference, Melbourne, USA, 10-12 March 2006
Publisher / Ed. Institution : ACM
Issue Date: 2006
License (according to publishing contract) : Licence according to publishing contract
Type of review: Not specified
Language : English
Subjects : Expert system; Quality assessment; Microarray
Subject (DDC) : 005: Computer programming, programs and data
570: Biology
Abstract: Computing reliable gene expression levels from microarray experiments is a sophisticated process with many potential pitfalls. Quality control is one of the most important steps in this process. We present a web based expert system for automatic quality assessment of Affymetrix GeneChip data. Our approach combines multiple quality metrics with supervised machine learning in order to identify data of low quality. Our system approximates expert opinion as represented in a knowledge base consisting of 41 microarray experiments with 352 CEL files annotated by a domain expert. GeneChips of low quality are detected automatically and can be excluded from subsequent analysis. This is especially important for large experiments or can assist the inexperienced users. Our expert system is fully implemented and integrated into a publicly available remote analysis computation engine for gene expression data.
Departement: School of Engineering
Organisational Unit: Institute of Data Analysis and Process Design (IDP)
Publication type: Conference paper
DOI : 10.1145/1185448.1185540
ISBN: 1-59593-315-8
URI: https://digitalcollection.zhaw.ch/handle/11475/14002
Appears in Collections:Publikationen School of Engineering

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