This repository contains code and manuscript files for the paper Overcoming systematic errors caused by log-transformation of normalized single-cell RNA sequencing data by Lun (2018).
The report subdirectory contains LaTeX files for the report.
The scripts subdirectory contains R code to reproduce the analyses described in the report:
spurious_sim.R, to examine the non-zero log-fold change induced by the log-transformation.substructure.R, to examine the introduction of structural artifacts due the log-transformation.alternatives.R, to examine the performance of other transformations.check_ercc.R, to examine the behaviour of the log-transformation on real data.power_sim.R, to examine the consequences on detection power with an increased pseudo-count.