IQRray, a new method for Affymetrix microarray quality control, and the homologous organ conservation score, a new benchmark method for quality control metrics.
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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DOI：
10.1093/bioinformatics/btu027
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发表时间：
2014-05-15
期刊：
影响因子：
--
通讯作者：
Robinson-Rechavi M
中科院分区：
文献类型：
--
作者：
Rosikiewicz M;Robinson-Rechavi M
动机：积累在公共存储库中的微阵列结果在元分析研究和二级数据库中被广泛重用。利用该技术获得的数据质量因实验而异，需要一种有效的质量评估方法来保证数据的可靠性。结果：缺乏一个良好的基准，阻碍了现有质量控制方法的评价。在这项研究中，我们提出了一种新的基于表达谱进化守恒的独立质量度量。通过使用11个大型器官特异性数据集，我们发现，在测试的14个指标中，我们开发的新质量指标IQRray与该参考指标的相关性最高。在由多个独立实验的阵列组成的数据集中，iqarray在识别质量较差的阵列方面优于其他方法。相比之下，在单个实验中检测异常值的方法（如归一化未缩放标准误差和相对对数表达式）的性能较低，因为这些方法无法检测仅包含低质量数组的数据集，并且无法直接比较实验之间的分数。可用性和实现：IQRray的R实现可在：ftp://lausanne.isb-sib.ch/pub/databases/Bgee/general/IQRray.R获得。补充信息：补充数据可在Bioinformatics在线获取。
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.
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