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The importance of study design for detecting differentially abundant features in high-throughput experiments

Luo, H., Li, J., Chia, B.K.H. et al.

High-throughput assays, such as RNA-seq, to detect differential abundance are widely used. Variable performance across statistical tests, normalizations, and conditions leads to resource wastage and reduced sensitivity. EDDA represents a first, general design tool for RNA-seq, NanoString®, and metagenomic analysis, that rationally selects tests, predicts performance, and plans experiments to minimize resource wastage. Case studies highlight EDDA’s ability to model single-cell RNA-seq, suggesting ways to reduce sequencing costs up to five-fold and improving metagenomic biomarker detection through improved test selection. EDDA’s novel mode-based normalization for detecting differential abundance improves robustness by 10% to 20% and precision by up to 140%.

Citation

Luo, H., Li, J., Chia, B.K.H. et al. "The importance of study design for detecting differentially abundant features in high-throughput experiments" Genome Biology (2014): 527