Robustness and resilience of computational deconvolution methods for bulk RNA sequencing data

This study benchmarks the robustness and resilience of computational deconvolution methods for estimating cell-type proportions in bulk tissues, with a focus on comparing reference-based and reference-free methods. Robustness is evaluated by generating in silico pseudo-bulk tissue RNA sequencing data from cell-level gene expression profiles derived from four different tissue types, with simulated cellular composition at varying levels of heterogeneity. To assess resilience, we intentionally alter single-cell RNA profiles to create pseudo-bulk tissue RNA-seq data. Deconvolution estimates are compared with ground truth using Pearson's correlation coefficient, root mean squared deviation, and mean absolute deviation. The results show that reference-based methods are more robust when reliable reference data are available, whereas reference-free methods excel in scenarios lacking suitable reference data. Furthermore, variations in cell-level transcriptomic profiles and cell composition have emerged as critical factors influencing the performance of deconvolution methods. This study provides significant insights into the factors affecting bulk tissue deconvolution performance, which are essential for guiding users and advancing the development of more powerful and reliable algorithms in the future.