In Papyro Comparison of TMM (edgeR), RLE (DESeq2), and MRN Normalization Methods for a Simple Two-Conditions-Without-Replicates RNA-Seq Experimental Design.
In the past 5 years, RNA-Seq has become a powerful tool in transcriptome analysis even though computational methods dedicated to the analysis of high-throughput sequencing data are yet to be standardized. It is, however, now commonly accepted that the choice of a normalization procedure is an important step in such a process, for example in differential gene expression analysis. The present article highlights the similarities between three normalization methods: TMM from edgeR R package, RLE from DESeq2 R package, and MRN. Both TMM and DESeq2 are widely used for differential gene expression analysis. This paper introduces properties that show when these three methods will give exactly the same results. These properties are proven mathematically and illustrated by performingin silicocalculations on a given RNA-Seq data set.
Genomics and Biotechnology of the Fruits Laboratory, UMR 990 INRA/Institut National Polytechnique de Toulouse, Ecole Nationale Supérieure Agronomique de Toulouse, Université de Toulouse Castanet-Tolosan, France.
Elie
E
Maza
DESeq2; RNA-seq data; comparison of methods; edgeR; normalization
Nat Rev Genet. 2009 Jan;10(1):57-63
19015660
BMC Bioinformatics. 2013 Mar 09;14:91
23497356
Commun Integr Biol. 2013 Nov 1;6(6):e25849
26442135
Bioinformatics. 2010 Jan 1;26(1):139-40
19910308
BMC Genomics. 2016 Jan 05;17:28
26732976
Nat Biotechnol. 2014 Sep;32(9):896-902
25150836
Biomed Res Int. 2015;2015:621690
26176014
Algorithms Mol Biol. 2012 Apr 05;7(1):5
22475125
Genome Biol. 2010;11(10):R106
20979621
Nat Protoc. 2013 Sep;8(9):1765-86
23975260
BMC Bioinformatics. 2015 Oct 28;16:347
26511205
Genome Biol. 2004;5(10):R80
15461798
Brief Bioinform. 2013 Nov;14(6):671-83
22988256
Genome Biol. 2010;11(3):R25
20196867
Genome Biol. 2013;14(9):R95
24020486
BMC Bioinformatics. 2010 Feb 18;11:94
20167110
BMC Bioinformatics. 2013 Jul 09;14:219
23837715
BMC Bioinformatics. 2015 Nov 04;16:361
26538400
Genome Biol. 2014;15(12):550
25516281