Shimokawa Kazuro, Kodzius Rimantas, Matsumura Yonehiro, Hayashizaki Yoshihide
CSH Protoc. 2008 Feb 1;2008:pdb.prot4937. doi: 10.1101/pdb.prot4937.
INTRODUCTIONIn terms of cost per measurement, the use of DNA microarrays for comprehensive and quantitative expression measurements is vastly superior to other methods such as Northern blotting or quantitative reverse transcriptase polymerase chain reaction (QRT-PCR). However, the output values of DNA microarrays are not always highly reliable or accurate compared with other techniques, and the output data sometimes consist of measurements of relative expression (treated sample vs. untreated) rather than absolute expression values as desired. In effect, some measurements from some laboratories do not represent absolute expression values (such as the number of transcripts) and as such are experimentally deficient. This protocol addresses one problem in some microarray data: the absence of accurate measurements. Spot reliability evaluation score for DNA microarrays (SRED) offers a reliability value for each spot in the microarray. SRED does not require an entire microarray to assess the reliability, but rather analyzes the reliability of individual spots of the microarray. The calculation of a reliability index can be used for different microarray systems, which facilitates the analysis of multiple microarray data sets from different experimental platforms.
引言
就每次测量的成本而言，使用DNA微阵列进行全面定量表达测量比其他方法（如Northern印迹法或定量逆转录聚合酶链反应（QRT-PCR））具有极大优势。然而，与其他技术相比，DNA微阵列的输出值并不总是高度可靠或准确，并且输出数据有时是相对表达（处理样本与未处理样本）的测量值，而不是所需的绝对表达值。实际上，一些实验室的某些测量结果并不代表绝对表达值（如转录本数量），因此在实验上存在缺陷。本方案解决了一些微阵列数据中的一个问题：缺乏准确测量。DNA微阵列斑点可靠性评估得分（SRED）为微阵列中的每个斑点提供一个可靠性值。SRED不需要整个微阵列来评估可靠性，而是分析微阵列中各个斑点的可靠性。可靠性指数的计算可用于不同的微阵列系统，这有助于分析来自不同实验平台的多个微阵列数据集。
