Pavlidis Paul, Li Qinghong, Noble William Stafford
Columbia Genome Center, Columbia University, 1150 St Nicholas Avenue, New York, NY 10032, USA.
Bioinformatics. 2003 Sep 1;19(13):1620-7. doi: 10.1093/bioinformatics/btg227.
We examine the effect of replication on the detection of apparently differentially expressed genes in gene expression microarray experiments. Our analysis is based on a random sampling approach using real data sets from 16 published studies. We consider both the ability to find genes that meet particular statistical criteria as well as the stability of the results in the face of changing levels of replication.
While dependent on the data source, our findings suggest that stable results are typically not obtained until at least five biological replicates have been used. Conversely, for most studies, 10-15 replicates yield results that are quite stable, and there is less improvement in stability as the number of replicates is further increased. Our methods will be of use in evaluating existing data sets and in helping to design new studies.
我们研究了重复实验对基因表达微阵列实验中明显差异表达基因检测的影响。我们的分析基于一种随机抽样方法，使用了来自16项已发表研究的真实数据集。我们既考虑了找到符合特定统计标准的基因的能力，也考虑了面对重复水平变化时结果的稳定性。
虽然依赖于数据源，但我们的研究结果表明，通常至少使用五个生物学重复才能获得稳定的结果。相反，对于大多数研究来说，10 - 15个重复产生的结果相当稳定，并且随着重复次数的进一步增加，稳定性的提高较少。我们的方法将有助于评估现有数据集以及设计新的研究。
