Department of Biochemistry, Department of Biostatistics, State University of New York at Buffalo, Buffalo, NY 14214, USA.
Bioinformatics. 2011 May 1;27(9):1284-9. doi: 10.1093/bioinformatics/btr135. Epub 2011 Mar 16.
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.
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.
The Ag Spike raw data can be accessed at http://www.ccr.buffalo.edu/halfon/spike/index.html and through NCBI's Gene Expression Omnibus (GEO; accession GSE24866).
Spike-in 数据集为评估和比较竞争的微阵列分析策略提供了有价值的资源。我们之前完全定义的 Spike-in 数据集，即 Golden 和 Platinum Spikes，为 Affymetrix GeneChips 的分析提供了一些见解。然而，对于双色平台，一直没有类似的数据集，其中所有 cRNA 的身份和相对水平都是预先确定的。
我们为 Agilent 微阵列生成了一个完全定义的 Spike-in 数据集，其中包含 12 个阵列，超过 2000 个差异表达，以及大约 3600 个背景 cRNA。这个“Ag Spike”数据集的组成与我们之前的 Platinum Spike 数据集相同，因此允许直接进行跨平台比较。我们在这里展示了 Ag Spike 数据集用于评估专为双色阵列设计的不同分析方法的效用。Ag Spike 和 Platinum Spike 研究之间的比较表明，使用 Affymetrix 和 Agilent 平台获得的结果之间具有高度一致性。
Ag Spike 的原始数据可在 http://www.ccr.buffalo.edu/halfon/spike/index.html 上访问，并可通过 NCBI 的基因表达综合数据库（GEO；注册号 GSE24866）访问。
