A wholly defined Agilent microarray spike-in dataset
A wholly defined Agilent microarray spike-in dataset
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DOI：
10.1093/bioinformatics/btr135
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发表时间：
2011-05-01
期刊：
影响因子：
5.8
通讯作者：
Halfon, Marc S.
中科院分区：
文献类型：
--
作者：
Zhu, Qianqian;Miecznikowski, Jeffrey C.;Halfon, Marc S.
动机：Spike-in 数据集为评估和比较竞争性微阵列分析策略提供了宝贵的资源。我们之前完全定义的尖峰数据集（黄金尖峰和白金尖峰）为 Affymetrix GeneChips 的分析提供了见解。然而，双色平台还没有一个类似的数据集，其中所有 cRNA 身份和相对水平都是已知的。 结果：我们为安捷伦微阵列生成了一个完整定义的掺入数据集，该数据集由 12 个阵列组成，具有 2000 多个差异表达和大约 3600 个背景 cRNA。此“Ag Spike”数据集的组成与我们之前的 Platinum Spike 数据集的组成相同，因此允许直接跨平台比较。我们在这里展示了 Ag Spike 数据集用于评估为双色阵列设计的不同分析方法的实用性。 Ag Spike 和 Platinum Spike 研究之间的比较表明，使用 Affymetrix 和 Agilent 平台获得的结果高度一致。
Motivation: Spike-in datasets provide a valuable resource for assessing and comparing among competing microarray analysis strategies. Our previous wholly defined spike-in datasets, the Golden and Platinum Spikes, have provided insights for the analysis of Affymetrix GeneChips. However, a similar dataset, in which all cRNA identities and relative levels are known prospectively, has not been available for two-color platforms.Results: We have generated a wholly defined spike-in dataset for Agilent microarrays consisting of 12 arrays with more than 2000 differentially expressed, and approximately 3600 background, cRNAs. The composition of this 'Ag Spike' dataset is identical to that of our previous Platinum Spike dataset and therefore allows direct cross-platform comparison. We demonstrate here the utility of the Ag Spike dataset for evaluating different analysis methods designed for two-color arrays. Comparison between the Ag Spike and Platinum Spike studies shows high agreement between results obtained using the Affymetrix and Agilent platforms.