title: MultiRankSeq: multiperspective approach for RNAseq differential expression analysis and quality control.
abstract: After a decade of microarray technology dominating the field of high-throughput gene expression profiling, the introduction of RNAseq has revolutionized gene expression research. While RNAseq provides more abundant information than microarray, its analysis has proved considerably more complicated. To date, no consensus has been reached on the best approach for RNAseq-based differential expression analysis. Not surprisingly, different studies have drawn different conclusions as to the best approach to identify differentially expressed genes based upon their own criteria and scenarios considered. Furthermore, the lack of effective quality control may lead to misleading results interpretation and erroneous conclusions. To solve these aforementioned problems, we propose a simple yet safe and practical rank-sum approach for RNAseq-based differential gene expression analysis named MultiRankSeq. MultiRankSeq first performs quality control assessment. For data meeting the quality control criteria, MultiRankSeq compares the study groups using several of the most commonly applied analytical methods and combines their results to generate a new rank-sum interpretation. MultiRankSeq provides a unique analysis approach to RNAseq differential expression analysis. MultiRankSeq is written in R, and it is easily applicable. Detailed graphical and tabular analysis reports can be generated with a single command line.
authors: Center for Quantitative Sciences, Vanderbilt University, Nashville, TN 37027, USA.
authors: Yan
authors: 0000-0001-5252-3960
authors: Y
authors: Guo
authors: Center for Quantitative Sciences, Vanderbilt University, Nashville, TN 37027, USA.
authors: Shilin
authors: 0000-0002-3787-8111
authors: S
authors: Zhao
authors: Center for Quantitative Sciences, Vanderbilt University, Nashville, TN 37027, USA.
authors: Fei
authors: F
authors: Ye
authors: Center for Quantitative Sciences, Vanderbilt University, Nashville, TN 37027, USA.
authors: Quanhu
authors: 0000-0001-8951-9295
authors: Q
authors: Sheng
authors: Center for Quantitative Sciences, Vanderbilt University, Nashville, TN 37027, USA.
authors: Yu
authors: 0000-0003-2086-9670
authors: Y
authors: Shyr
mesh_terms: D000465:Algorithms; D016000:Cluster Analysis; D019295:Computational Biology / Q000379:methods; D030541:Databases, Genetic; D020869:Gene Expression Profiling; D006801:Humans; D020411:Oligonucleotide Array Sequence Analysis; D011786:Quality Control; D015203:Reproducibility of Results; D017423:Sequence Analysis, RNA / Q000379:methods*