cDNA芯片重复探针检测值的一致性分析

Analysis of measurement consistency of replicate probes in cDNA microarrays

通过SOURCE数据库对4套cDNA数据的探针进行了注释,分析了对应同一条Unigene的多个探针的检测值(即重复检测值)之间的相关性。采用两种常规方法处理了重复检测值,比较了这两种处理方法对筛选差异表达基因的影响。结果显示:Unigene的重复检测值之间存在一定比例的负相关;更新探针注释数据后的重复检测值之间的低相关比例减少,高相关比例显著提高;重复点样探针之间的相关性高于其它重复检测值,但是仍有很多低相关;两种处理重复检测值方法对于用基因表达差异显著性分析方法(SAM)与T检验方法筛选差异表达基因影响不大。

The probes relevant to four cDNA microarray datasets were annotated through the SOURCE database, and the correlativity of measurements from multiple probes mapped to a same Unigene was analysed. Also the Pearson correlation coefficients for multiply measured probes were computed. Based on two different methods which are usually used to deal with the expression values of multiple probes mapped to one Unigene, the differentially expressed genes （DEGs）selected by the significance analysis of microarray （SAM） or T-test were analyzed and compared. The results show that the correlation can be greatly improved when using updated annotations of probes. With replicate probes treated by the two different methods, little difference between the DEGs selected from each dataset is observed.