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

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. Pl...

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Detalles Bibliográficos
Autores principales: McGregor, Kevin, Labbe, Aurélie, Greenwood, Celia M. T.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2017
Materias:
Correspondence
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5282700/
https://www.ncbi.nlm.nih.gov/pubmed/28137287
http://dx.doi.org/10.1186/s13059-017-1149-7
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author McGregor, Kevin
Labbe, Aurélie
Greenwood, Celia M. T.
author_facet McGregor, Kevin
Labbe, Aurélie
Greenwood, Celia M. T.
author_sort McGregor, Kevin
collection PubMed
description 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
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spelling pubmed-52827002017-02-03 Response to: Correcting for cell-type effects in DNA methylation studies: reference-based method outperforms latent variable approaches in empirical studies McGregor, Kevin Labbe, Aurélie Greenwood, Celia M. T. Genome Biol Correspondence 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 BioMed Central 2017-01-30 /pmc/articles/PMC5282700/ /pubmed/28137287 http://dx.doi.org/10.1186/s13059-017-1149-7 Text en © The Author(s). 2017 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Correspondence
McGregor, Kevin
Labbe, Aurélie
Greenwood, Celia M. T.
Response to: Correcting for cell-type effects in DNA methylation studies: reference-based method outperforms latent variable approaches in empirical studies
title Response to: Correcting for cell-type effects in DNA methylation studies: reference-based method outperforms latent variable approaches in empirical studies
title_full Response to: Correcting for cell-type effects in DNA methylation studies: reference-based method outperforms latent variable approaches in empirical studies
title_fullStr Response to: Correcting for cell-type effects in DNA methylation studies: reference-based method outperforms latent variable approaches in empirical studies
title_full_unstemmed Response to: Correcting for cell-type effects in DNA methylation studies: reference-based method outperforms latent variable approaches in empirical studies
title_short Response to: Correcting for cell-type effects in DNA methylation studies: reference-based method outperforms latent variable approaches in empirical studies
title_sort response to: correcting for cell-type effects in dna methylation studies: reference-based method outperforms latent variable approaches in empirical studies
topic Correspondence
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5282700/
https://www.ncbi.nlm.nih.gov/pubmed/28137287
http://dx.doi.org/10.1186/s13059-017-1149-7
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