Brettschneider, Julia, Collin, Francois, Bolstad, Benjamin M. and Speed, T. P.. (2008) Quality assessment for short oligonucleotide microarray data. Technometrics, Volume 50 (Number 3). pp. 241-264. ISSN 0040-1706

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Abstract

Quality of microarray gene expression data has emerged as a new research topic. As in other areas, microarray quality is assessed by comparing suitable numerical summaries across microarrays, so that outliers and trends can be visualized and poor-quality arrays or variable quality sets of arrays can be identified. Because each single array Comprises tens or hundreds of thousands of measurements, the challenge is to find numerical summaries that can be used to make accurate quality calls. Toward this end, several new quality measures are introduced based on probe-level and probeset-level information, all obtained as it byproduct of the low-level analysis algorithms RMA/fitPLM for Affymetrix GeneChips. Quality landscapes spatially localize chip or hybridization problems. Numerical chip quality measures are derived from the distribution of normalized unsealed standard errors and relative log expressions. Quality of chip batches is assessed by residual scale factors. These quality assessment measures are demonstrated on a variety of data sets, including spike-in experiments, small lab experiments, and multisite studies. They are compared with Affymetrix's individual chip quality report.

Item Type:	Journal Article
Subjects:	Q Science > QP Physiology
Divisions:	Faculty of Science > Statistics
Library of Congress Subject Headings (LCSH):	DNA microarrays -- Quality control -- Statistical methods, Oligonucleotides
Journal or Publication Title:	Technometrics
Publisher:	American Statistical Association
ISSN:	0040-1706
Date:	August 2008
Volume:	Volume 50
Number:	Number 3
Number of Pages:	24
Page Range:	pp. 241-264
Identification Number:	10.1198/004017008000000334
Status:	Peer Reviewed
Publication Status:	Published
Access rights to Published version:	Restricted or Subscription Access
Funder:	National Institutes of Health (U.S.) (NIH)
Grant number:	2P50MH060398 (NIH)
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URI:	http://wrap.warwick.ac.uk/id/eprint/28553

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