Background: Deconvolution is a mathematical process of resolving an observed function into its constituent elements from which the signal was formed. In the field of biomedical research, deconvolution analysis is applied to obtain single cell-type or tissue specific signatures from a mixed signal. Recent development of next generation sequencing technology suggests RNA-seq as a fast and accurate method for obtaining transcriptomic profiles. Although linearity assumption is required in most of deconvolution algorithms, few studies have been conducted to investigate which RNA-seq quantification methods 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 parameters 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.
['Haijing Jin', 'Ying-Wooi Wan', 'Zhandong Liu']
Comprehensive Evaluation of RNA-seq Quantification Methods for Linearity