Fig. 1

Platform effect between scRNA-seq and targeted spatial transcriptomics technologies. A–C Scatter plot showing the log transformed relative expression of genes measured by both scRNA-seq and targeted spatial transcriptomics across three datasets, Moffit (A), Codeluppi (B), and Zhang (C), respectively. A small value is added to avoid negative infinity after log transformation. Each dot represents the relative expression of one gene in one cell type. Denominator for relative expression calculation is from all genes measured by both technologies. Color indicates density of dots. Dots should fall on the diagonal when there is no platform effect. D Density plot of Deming regression coefficient for each dataset. Deming regression is fitted for each gene using relative expression measured by scRNA-seq and spatial transcriptomics data with intercept fixed to 0. E Posterior predictive check of the Bayesian models fitted using each of the three datasets. QQ plot showing the distribution of simulated vs. observed spatial transcriptomics measurements. F,G Density plot showing the estimated posterior distribution of σγ (F) and σc (G)