cDNA微阵列的标准化方法研究  

Study on Normalization Method for cDNA Microarray Data

作　　者：张纪刚[1] 张勤[1] 殷宗俊[1] 

机构地区：[1]中国农业大学动物科技学院,北京100094

出　　处：《农业生物技术学报》2006年第3期356-359,共4页Journal of Agricultural Biotechnology

基　　金：国家重点基础研究发展规划(973)(No.G2000016103);国家高技术研究与发展计划(863)(No:2001AA243011)资助。

摘　　要：针对目前通用的cDNA微阵列数据的标准化处理方法(常称为对数比转换法)中存在的缺陷,提出了一种新的cDNA微阵列数据标准化方法-非转换法。该方法利用Huber等(2003)提出的芯片数据分析模型,在对芯片背景进行校正后,根据最小二乘估计原理,通过迭代的方式直接对样品中的基因转录水平进行估计,从而达到数据标准化的目的。利用计算机模拟,比较了在各种条件下(不同的芯片内探针重复数、不同的背景变异程度、不同的差异表达基因上下调比例等)该方法与对数比转换法的优劣。结果表明,在所有条件下,非转换法都优于对数比转化法,由非转换法得到的估计值的相对偏差都在5%以下,而由对数比转化法得到的估计值的相对偏差都在20%以上,而且对数比转化法对背景变异和差异表达基因上下调比例更敏感,随着背景变异程度的增大和差异表达基因上下调比例不对称性的提高,其估计值的偏差急剧上升,而非转换法则基本不受影响。因而非转换法可以作为cDNA微阵列数据标准化的一种替代方法。In view of the limitations of the currently widely used method for the cDNA microarray data standardization （often called log-ratio transformation method）, a new method was proposed which named as non-transformation method. It does not transform the data but directly estimates the gene transcription level after correction of the background effect based on Huber＇s model and principle of least square estimation through an iteration process. Using computer simulation, the new method was compared with the log-ratio method under various conditions （different number of repeated probes on a chip, different background variation, and different ratio of up- and dawn-regulated expressed genes）. The results showed that in all conditions the non-transformation method performed better than the log-ratio method. The relative biases from the non-transformation method were less than 5%, while those from the log-ratio method more than 20%. Furthermore, the log-ratio method was very sensitive to the background variation and the ratio of up- and dawn-regulated expressed genes. With the increase of the background variation or the unbalance level of the ratio of up- and dawn-regulated expressed genes, the biases from the log-ratio method increased rapidly, while the non-transformation method was almost not influenced by these factors. Therefore, the non-transformation method could be used as an alternative method for cDNA microarray data standardization

关 键 词：CDNA微阵列 标准化方法 差异表达基因 最小二乘估计 数据标准化 转换法 标准化处理 计算机模拟 转化法 估计值 

分 类 号：S814[农业科学—畜牧学]