IQRray, a new method for Affymetrix microarray quality control, and the homologous organ conservation score, a new benchmark method for quality control metrics.

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Serval ID
serval:BIB_0E5C20608CA6
Type
Article: article from journal or magazin.
Collection
Publications
Title
IQRray, a new method for Affymetrix microarray quality control, and the homologous organ conservation score, a new benchmark method for quality control metrics.
Journal
Bioinformatics
Author(s)
Rosikiewicz M., Robinson-Rechavi M.
ISSN
1367-4811 (Electronic)
ISSN-L
1367-4803
Publication state
Published
Issued date
2014
Peer-reviewed
Oui
Volume
30
Number
10
Pages
1392-1399
Language
english
Abstract
MOTIVATION: Microarray results accumulated in public repositories are widely reused in meta-analytical studies and secondary databases. The quality of the data obtained with this technology varies from experiment to experiment, and an efficient method for quality assessment is necessary to ensure their reliability.
RESULTS: The lack of a good benchmark has hampered evaluation of existing methods for quality control. In this study, we propose a new independent quality metric that is based on evolutionary conservation of expression profiles. We show, using 11 large organ-specific datasets, that IQRray, a new quality metrics developed by us, exhibits the highest correlation with this reference metric, among 14 metrics tested. IQRray outperforms other methods in identification of poor quality arrays in datasets composed of arrays from many independent experiments. In contrast, the performance of methods designed for detecting outliers in a single experiment like Normalized Unscaled Standard Error and Relative Log Expression was low because of the inability of these methods to detect datasets containing only low-quality arrays and because the scores cannot be directly compared between experiments.
AVAILABILITY AND IMPLEMENTATION: The R implementation of IQRray is available at: ftp://lausanne.isb-sib.ch/pub/databases/Bgee/general/IQRray.R.
CONTACT: Marta.Rosikiewicz@unil.ch
SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
Pubmed
Web of science
Open Access
Yes
Create date
09/10/2013 11:32
Last modification date
20/08/2019 12:35
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