Transformation and Preprocessing of Single-Cell RNA-Seq Data

The count table, a numeric matrix of genes × cells, is a basic input data structure in the analysis of single-cell RNA-seq data. A common preprocessing step is to adjust the counts for variable sampling efficiency and to transform them so that the variance is similar across the dynamic range. These steps are intended to make subsequent application of generic statistical methods more palatable. Here, we describe three transformations (based on the delta method, model residuals, or inferred latent expression state) and compare their strengths and weaknesses. We conclude with an outlook on future needs for the development of transformations for single-cell count data.