Letter to the Editor response: Nygaard et al.

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.