van Hijum Sacha A F T, de Jong Anne, Baerends Richard J S, Karsens Harma A, Kramer Naomi E, Larsen Rasmus, den Hengst Chris D, Albers Casper J, Kok Jan, Kuipers Oscar P
Department of Molecular Genetics, University of Groningen, Groningen Biomolecular Sciences and Biotechnology Institute, PO Box 14, 9750 AA Haren, The Netherlands.
BMC Genomics. 2005 May 20;6:77. doi: 10.1186/1471-2164-6-77.
In research laboratories using DNA-microarrays, usually a number of researchers perform experiments, each generating possible sources of error. There is a need for a quick and robust method to assess data quality and sources of errors in DNA-microarray experiments. To this end, a novel and cost-effective validation scheme was devised, implemented, and employed.
A number of validation experiments were performed on Lactococcus lactis IL1403 amplicon-based DNA-microarrays. Using the validation scheme and ANOVA, the factors contributing to the variance in normalized DNA-microarray data were estimated. Day-to-day as well as experimenter-dependent variances were shown to contribute strongly to the variance, while dye and culturing had a relatively modest contribution to the variance.
Even in cases where 90% of the data were kept for analysis and the experiments were performed under challenging conditions (e.g. on different days), the CV was at an acceptable 25%. Clustering experiments showed that trends can be reliably detected also from genes with very low expression levels. The validation scheme thus allows determining conditions that could be improved to yield even higher DNA-microarray data quality.
在使用DNA微阵列的研究实验室中，通常有许多研究人员进行实验，每个人都会产生可能的误差来源。因此需要一种快速且可靠的方法来评估DNA微阵列实验中的数据质量和误差来源。为此，设计、实施并采用了一种新颖且具有成本效益的验证方案。
对基于乳酸乳球菌IL1403扩增子的DNA微阵列进行了多项验证实验。使用该验证方案和方差分析，估计了导致标准化DNA微阵列数据方差的因素。结果表明，日常方差以及实验者相关方差对方差有很大贡献，而染料和培养对方差的贡献相对较小。
即使在90%的数据用于分析且实验在具有挑战性的条件下进行（例如在不同日期）的情况下，变异系数（CV）仍处于可接受的25%。聚类实验表明，即使是表达水平非常低的基因，其趋势也能被可靠地检测到。因此，该验证方案可以确定哪些条件可以改进，以获得更高质量的DNA微阵列数据。
