A generally applicable validation scheme for the assessment of factors involved in reproducibility and quality of DNA-microarray data.
A generally applicable validation scheme for the assessment of factors involved in reproducibility and quality of DNA-microarray data.
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DOI：
10.1186/1471-2164-6-77
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发表时间：
2005-05-20
期刊：
影响因子：
4.4
通讯作者：
Kuipers OP
中科院分区：
文献类型：
--
作者：
van Hijum SA;de Jong A;Baerends RJ;Karsens HA;Kramer NE;Larsen R;den Hengst CD;Albers CJ;Kok J;Kuipers OP
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，每个实验都可能产生误差。有一个快速和强大的方法来评估DNA微阵列实验中的数据质量和错误来源的需要。为此，一种新颖的和具有成本效益的验证方案的设计，实施和使用。在基于乳酸乳球菌IL 1403扩增子的DNA微阵列上进行了许多验证实验。使用验证方案和方差分析，因素的方差在归一化的DNA微阵列数据进行了估计。日复一日，以及实验依赖性的方差被证明有助于强烈的方差，而染料和培养有一个相对温和的方差的贡献。即使在保留90%的数据用于分析并且在挑战性条件下（例如在不同日期）进行实验的情况下，CV也在可接受的25%。聚类实验表明，趋势也可以可靠地检测到非常低的表达水平的基因。因此，验证方案允许确定可以改进以产生甚至更高的DNA微阵列数据质量的条件。
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.
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影响因子：
5.8
作者：
van Hijum, SAFT;de Jong, A;Kuipers, OP
通讯作者：
Kuipers, OP
DOI：
10.1023/a:1020691801251
发表时间：
2002-08-01
影响因子：
2.6
作者：
Kuipers, OP;de Jong, A;Kok, J
通讯作者：
Kok, J
影响因子：
4.8
作者：
Piper, MDW;Daran-Lapujade, P;Pronk, JT
通讯作者：
Pronk, JT
影响因子：
5.8
作者：
de la Nava, JG;van Hijum, S;Trelles, O
通讯作者：
Trelles, O
影响因子：
4.8
作者：
Long, AD;Mangalam, HJ;Baldi, P
通讯作者：
Baldi, P