Separating measurement and expression models clarifies confusion in single-cell RNA sequencing analysis.

ABSTRACT: The high proportion of zeros in typical single-cell RNA sequencing datasets has led to widespread but inconsistent use of terminology such as dropout and missing data. Here, we argue that much of this terminology is unhelpful and confusing, and outline simple ideas to help to reduce confusion. These include: (1) observed single-cell RNA sequencing counts reflect both true gene expression levels and measurement error, and carefully distinguishing between these contributions helps to clarify thinking; and (2) method development should start with a Poisson measurement model, rather than more complex models, because it is simple and generally consistent with existing data. We outline how several existing methods can be viewed within this framework and highlight how these methods differ in thei

SUBMITTER: Sarkar A 

PROVIDER: S-EPMC8370014 | biostudies-literature | 2021 Jun

REPOSITORIES: biostudies-literature