title: Comprehensive evaluation of RNA-seq quantification methods for linearity.
abstract: BACKGROUND
  Deconvolution is a mathematical process of resolving an observed function into its constituent elements. In the field of biomedical research, deconvolution analysis is applied to obtain single cell-type or tissue specific signatures from a mixed signal and most of them follow the linearity assumption. Although recent development of next generation sequencing technology suggests RNA-seq as a fast and accurate method for obtaining transcriptomic profiles, few studies have been conducted to investigate best RNA-seq quantification methods that yield the optimum linear space for deconvolution analysis.
  
  
  RESULTS
  Using a benchmark RNA-seq dataset, we investigated the linearity of abundance estimated from seven most popular RNA-seq quantification methods both at the gene and isoform levels. Linearity is evaluated through parameter estimation, concordance analysis and residual analysis based on a multiple linear regression model. Results show that count data gives poor parameter estimations, large intercepts and high inter-sample variability; while TPM value from Kallisto and Salmon shows high linearity in all analyses.
  
  
  CONCLUSIONS
  Salmon and Kallisto TPM data gives the best fit to the linear model studied. This suggests that TPM values estimated from Salmon and Kallisto are the ideal RNA-seq measurements for deconvolution studies.
authors.affiliation: Graduate Program in Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, One Baylor Plaza, Houston, 77030, TX, USA.
authors.forename: Haijing
authors.initials: H
authors.lastname: Jin
authors.affiliation: Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, 77030, TX, USA.
authors.forename: Ying-Wooi
authors.initials: YW
authors.lastname: Wan
authors.affiliation: Department of Pediatrics-Neurology, Jan and Dan Duncan Neurological Research Institute, Baylor College of Medicine, 1250 Moursund St., Suite 1325, Houston, 77030, TX, USA. zhandonl@bcm.edu.
authors.forename: Zhandong
authors.initials: Z
authors.lastname: Liu
mesh_terms: D003198:Computer Simulation; D020869:Gene Expression Profiling / Q000379:methods*; D015894:Genome, Human; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D016014:Linear Models; D020033:Protein Isoforms; D012313:RNA / Q000032:analysis* / Q000235:genetics; D017423:Sequence Analysis, RNA / Q000379:methods*; D059467:Transcriptome
chemical_list: D020033:Protein Isoforms; D012313:RNA
keywords: Deconvolution; Linearity; RNA-seq