Differential expression analysis in single-cell and spatial RNA-seq without model assumptions

Gene up(down)regulation findings in single cell and spatial RNASeq can be inconsistent despite remarkable progress in technology. False findings in high-quality samples raise concerns about assumptions behind widely accepted data analysis approaches. We therefore propose a weighted averaging approach for data analysis without assuming anything besides randomness of technical noise. This approach is closely related to prior work on statistics of cluster-randomized experiments. We show that weighing transcript counts based on measured noise variances and utilizing weighted rather than standard unweighted tests reduces both false positive and false negative findings. Our approach eliminates the need for parametrizing data distributions and/or rescaling transcript counts, which may cause artifacts by distorting and biasing the data. The resulting analysis is less complex and produces more consistent differential gene expression estimates.