{"about":{"site":"https://codewithpapers.app","non_affiliation":"Code with Papers and Syntology are not affiliated with, endorsed by, or sponsored by Papers with Code, Meta, or the pwc-archive mirror.","licence":"CC BY-SA 4.0","licence_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","attribution":"https://codewithpapers.app/attribution","modified":"archive material modified by Syntology; see the attribution page"},"url":"/paper/issues-arising-from-benchmarking-single-cell","title":"Issues arising from benchmarking single-cell RNA sequencing imputation methods","arxiv_id":"1908.07084","date":"2019-08-19","proceeding":null,"authors":["Wei Vivian Li","Jingyi Jessica Li"],"abstract":"On June 25th, 2018, Huang et al. published a computational method SAVER on Nature Methods for imputing dropout gene expression levels in single cell RNA sequencing (scRNA-seq) data. Huang et al. performed a set of comprehensive benchmarking analyses, including comparison with the data from RNA fluorescence in situ hybridization, to demonstrate that SAVER outperformed two existing scRNA-seq imputation methods, scImpute and MAGIC. However, their computational analyses were based on semi-synthetic data that the authors had generated following the Poisson-Gamma model used in the SAVER method. We have therefore re-examined Huang et al.'s study. We find that the semi-synthetic data have very different properties from those of real scRNA-seq data and that the cell clusters used for benchmarking are inconsistent with the cell types labeled by biologists. We show that a reanalysis based on real scRNA-seq data and grounded on biological knowledge of cell types leads to different results and conclusions from those of Huang et al.","url_abs":"https://arxiv.org/abs/1908.07084v1","url_pdf":"https://arxiv.org/pdf/1908.07084v1.pdf","source":{"archive":"pwc-archive (Hugging Face), CC BY-SA 4.0","snapshot":"2025-07-28","licence_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","row_kind":"links_only","authors_date_abstract":"arXiv metadata, CC0 1.0 (https://info.arxiv.org/help/license), from the Kaggle arXiv metadata snapshot of 2026-09-12"},"code_links":[{"paper_slug":"issues-arising-from-benchmarking-single-cell","repo_url":"https://github.com/Vivianstats/scImpute","is_official":1,"mentioned_in_paper":1,"mentioned_in_github":1,"framework":"none","reach":null}],"tasks":[],"methods":[],"datasets_introduced":[],"methods_introduced":[],"results":[],"syntology":{"atlas_url":null,"mcp":null,"developers":"https://syntology.ai/developers"},"arxiv_metadata":null,"syntology_extracted_results":null}