Here are the Three Differential Expression Analysis Methods for RNA Sequencing: limma, EdgeR, DESeq2 journals presenting the latest research across various disciplines. From social sciences to technology, each article is expected to provide valuable insights to our readers.
Shiyi Liu, Zitao Wang, Ronghui Zhu et al by MyJove Corporation in Journal of Visualized Experiments iss. 175 on October 5, 2021
RNA sequencing (RNA-seq) is one of the most widely used technologies in transcriptomics as it can reveal the relationship between the genetic alteration and complex biological processes and has great value in diagnostics, prognostics, and therapeutics of tumors. Differential analysis of RNA-seq data is crucial to identify aberrant transcriptions, and limma, EdgeR and DESeq2 are efficient tools for differential analysis. However, RNA-seq differential analysis requires certain skills with R language and the ability to choose an appropriate method, which is lacking in the curriculum of medical education. Herein, we provide the detailed protocol to identify differentially expressed genes (DEGs) between cholangiocarcinoma (CHOL) and normal tissues through limma, DESeq2 and EdgeR, respectively, and the results are shown in volcano plots and Venn diagrams. The three protocols of limma, DESeq2 and EdgeR are similar but have different steps among the processes of the analysis. For example, a linear model is used for statistics in limma, while the negative binomial distribution is used in edgeR and DESeq2. Additionally, the normalized RNA-seq count data is necessary for EdgeR and limma but is not necessary for DESeq2. Here, we provide a detailed protocol for three differential analysis methods: limma, EdgeR and DESeq2. The results of the three methods are partly overlapping. All three methods have their own advantages, and the choice of method only depends on the data.
journal：Journal of Visualized Experiments
Authors：Shiyi Liu; Zitao Wang; Ronghui Zhu; Feiyan Wang; Yanxiang Cheng; Yeqiang Liu
Published date：--
DOI：10.3791/62528
PDF link：https://www.jove.com/t/62528/three-differential-expression-analysis-methods-for-rna-sequencing
Article link：http://dx.doi.org/10.3791/62528
Article Source：MyJove Corporation。
