The growing complexity of biological experiment design based on high-throughput RNA sequencing (RNA-seq) is calling for more accommodative statistical tools. Researchers at Fudan University have developed a novel method, multiDE, for facilitating DE analysis using RNA-seq read count data with multiple treatment conditions. The read count is assumed to follow a log-linear model incorporating two factors (i.e., condition and gene), where an interaction term is used to quantify the association between gene and condition. The number of the degrees of freedom is reduced to one through the first order decomposition of the interaction, leading to a dramatically power improvement in testing DE genes when the number of conditions is greater than two. In their simulation situations, multiDE outperformed the benchmark methods (i.e. edgeR and DESeq2) even if the underlying model was severely misspecified, and the power gain was increasing in the number of conditions. In the application to two real datasets, multiDE identified more biologically meaningful DE genes than the benchmark methods.
Performance of various methods with simulation data based on the embryonic stem cells study. a False discovery rates; b ROC curves
Availability – An R package implementing multiDE is available publicly at http://homepage.fudan.edu.cn/zhangh/softwares/multiDE