Response to: Correcting for cell-type effects in DNA methylation studies: Reference-based method outperforms latent variable approaches in empirical studies

Abstract

We thank Hattab and colleagues for their correspondence and their investigation of cell-type mixture correction methods in methyl-CG binding domain sequencing. Here, we speculate on why surrogate variable analysis (SVA) performed differently between their two data sets, and poorly in one of them. Please see related Correspondence article: https://genomebiology.biomedcentral.com/articles/10/1186/s13059-017-1148-8and related Research article: https://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-0935-y