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

Kevin McGregor; Aurélie Labbe; Celia M T Greenwood

doi:10.1186/s13059-017-1149-7

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

Genome Biol. 2017 Jan 30;18(1):25. doi: 10.1186/s13059-017-1149-7.

Authors

Kevin McGregor^{1

2}, Aurélie Labbe³, Celia M T Greenwood^{4

5

6}

Affiliations

¹ Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, QC, Canada.
² Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montreal, QC, Canada.
³ Department of Decision Sciences, HEC Montreal, Montreal, QC, Canada.
⁴ Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, QC, Canada. [email protected].
⁵ Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montreal, QC, Canada. [email protected].
⁶ Departments of Oncology and Human Genetics, McGill University, Montreal, QC, Canada. [email protected].

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/s13059-017-1148-8 and related Research article: https://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-0935-y.

Publication types

Comment

MeSH terms

DNA Methylation*