Towfic F, Kusko R, Zeskind B
Biostatistics. 2017 Apr 1;18(2):197-199. doi: 10.1093/biostatistics/kxw031.
The article by Nygaard and others (2016) proposes that applying batch correction approaches to microarray data from studies with unbalanced designs may inadvertently exaggerate the differences observed. In seeking to illustrate their point, Nygaard and others (2016) utilized a dataset (GSE61901) from a study we published (Towfic and others, 2014) and showed that one analysis pipeline utilizing the traditional approach to batch correction (ComBat) yielded over 1000 differentially expressed probesets, while an alternative approach proposed by Nygaard and others (2016). (utilizing batch as a fixed effect and averaging technical replicates) recovered 11 differentially expressed probesets.
Nygaard等人（2016年）的文章提出，将批次校正方法应用于来自设计不均衡研究的微阵列数据可能会无意中夸大所观察到的差异。为了说明他们的观点，Nygaard等人（2016年）利用了我们发表的一项研究（Towfic等人，2014年）中的一个数据集（GSE61901），并表明一种采用传统批次校正方法（ComBat）的分析流程产生了超过1000个差异表达的探针集，而Nygaard等人（2016年）提出的另一种方法（将批次作为固定效应并对技术重复进行平均）仅发现了11个差异表达的探针集。
