Gene length corrected trimmed mean of M-values (GeTMM) processing of RNA-seq data performs similarly in intersample analyses while improving intrasample comparisons

Gene length corrected trimmed mean of M-values (GeTMM) processing of RNA-seq data performs similarly in intersample analyses while improving intrasample comparisons

Abstract Background Current normalization methods for RNA-sequencing data allow either for intersample comparison to identify differentially expressed (DE) genes or for intrasample comparison for the discovery and validation of gene signatures. Most studies on optimization of normalization methods t...

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Bibliographic Details
Main Authors: Marcel Smid, Robert R. J. Coebergh van den Braak, Harmen J. G. van de Werken, Job van Riet, Anne van Galen, Vanja de Weerd, Michelle van der Vlugt-Daane, Sandra I. Bril, Zarina S. Lalmahomed, Wigard P. Kloosterman, Saskia M. Wilting, John A. Foekens, Jan N. M. IJzermans, on behalf of the MATCH study group, John W. M. Martens, Anieta M. Sieuwerts
Format: Article
Language:English
Published: BMC 2018-06-01
Series:BMC Bioinformatics
Subjects:
RNA sequencing
Normalization methods
GeTMM
edgeR
TPM
DESeq2
Online Access:http://link.springer.com/article/10.1186/s12859-018-2246-7

Internet

http://link.springer.com/article/10.1186/s12859-018-2246-7

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