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首页> 外文期刊>Genomics >Spearman's footrule as a measure of cDNA microarray reproducibility.
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Spearman's footrule as a measure of cDNA microarray reproducibility.

机译：Spearman的法则作为cDNA微阵列可重复性的度量。

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Replication is a crucial aspect of microarray experiments, due to various sources of errors that persist even after systematic effects are removed. It has been confirmed that replication in microarray studies is not equivalent to duplication, and hence it is not a waste of scientific resources. Replication and reproducibility are the most important issues for microarray application in genomics. However, little attention has been p0aid to the assessment of reproducibility among replicates. Here we develop, using Spearman's footrule, a new measure of the reproducibility of cDNA microarrays, which is based on how consistently a gene's relative rank is maintained in two replicates. The reproducibility measure, termed index.R, has an R(2)-type operational interpretation. Index.R assesses reproducibility at the initial stage of the microarray data analysis even before normalization is done. We first define three layers of replicates, biological, technical, and hybridizational, which refer to different biological units, different mRNAs from the same tissue, and separate cDNAs from a cDNA pool. As the replicate layer moves down to a lower level, the experiment has fewer sources of errors and thus is expected to be more reproducible. To validate the method we apply index.R to two sets of controlled cDNA microarray experiments, each of which has two or three layers of replicates. Index.R shows a uniform increase as the layer of the replicates moves into a more homogeneous environment. We also note that index.R has a larger jump size than Pearson's correlation or Spearman's rank correlation for each replicate layer move, and therefore, it has greater expandability as a measure in [0,1] than these two other measures.
机译：复制是微阵列实验的关键方面，因为即使去除了系统影响，误差的各种来源仍然存在。已经证实，微阵列研究中的复制不等同于复制，因此也不浪费科学资源。复制和重现性是基因组学中微阵列应用最重要的问题。但是，很少有人关注复制品之间的可重复性评估。在这里，我们使用Spearman的规则开发了一种新的cDNA微阵列可重复性度量，该度量基于一个基因在两个重复样本中保持相对排名的一致性。称为index.R的可重复性度量具有R（2）类型的操作解释。即使在归一化之前，Index.R仍会在微阵列数据分析的初始阶段评估可重复性。我们首先定义了三层重复，生物学，技术和杂交，分别指不同的生物单位，来自同一组织的不同mRNA和来自cDNA库的cDNA。随着复制层下降到较低的水平，该实验的错误源更少，因此有望实现更高的可重复性。为了验证该方法，我们将index.R应用于两组受控cDNA微阵列实验，每组实验都有两到三层重复。随着复制品层移入更均匀的环境，Index.R显示均匀增加。我们还注意到，对于每个复制层移动，index.R的跳跃大小均大于Pearson相关性或Spearman秩相关性，因此，它在[0,1]中的度量比其他两个度量具有更大的可扩展性。

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