Coincidence between Transcriptome Analyses on Different Microarray Platforms Using a Parametric Framework
Coincidence between Transcriptome Analyses on Different Microarray Platforms Using a Parametric Framework
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DOI：
10.1371/journal.pone.0003555
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发表时间：
2008-10-29
期刊：
影响因子：
3.7
通讯作者：
Konagaya, Akihiko
中科院分区：
文献类型：
--
作者：
Konishi, Tomokazu;Konishi, Fumikazu;Konagaya, Akihiko
用于转录组数据分析的参数框架被证明在应用于使用两个不同的微阵列平台获取的数据时产生一致的结果。微阵列被广泛用于获取转录组信息，目前正在使用几个平台的芯片。然而，研究之间的差异经常被报道，特别是那些使用不同平台进行的研究，这让人对收集的数据的可靠性产生了怀疑。意见之间的不一致在很大程度上可归因于用于数据分析的分析框架之间的差异。现有的框架基于不同的理念，产生不同的结果，但都涉及根据要分析的数据确定的标准进行标准化。在本研究中，一个基于严格归一化模型的参数框架被应用于使用几个玻片类型芯片和基因芯片获取的数据。该模型基于微阵列数据的共同统计特征，并基于与该模型的线性关系对每组芯片数据进行归一化。在提出的框架中，观察到的表达变化和选择的基因在平台之间是一致的，与其他框架相比，实现了更好的数据普适性。
A parametric framework for the analysis of transcriptome data is demonstrated to yield coincident results when applied to data acquired using two different microarray platforms. Microarrays are widely employed to acquire transcriptome information, and several platforms of chips are currently in use. However, discrepancies among studies are frequently reported, particularly among those performed using different platforms, casting doubt on the reliability of collected data. The inconsistency among observations can be largely attributed to differences among the analytical frameworks employed for data analysis. The existing frameworks are based on different philosophies and yield different results, but all involve normalization against a standard determined from the data to be analyzed. In the present study, a parametric framework based on a strict model for normalization is applied to data acquired using several slide-glass-type chips and GeneChip. The model is based on a common statistical characteristic of microarray data, and each set of chip data is normalized on the basis of a linear relationship with this model. In the proposed framework, the expressional changes observed and genes selected are coincident between platforms, achieving superior universality of data compared to other frameworks.