Fig. 3

Application of batch correction techniques at the supercell level. A A Multidimensional Scaling (MDS) plot showcasing the variation in uncorrected single cells, supercells, and supercells that have been batch corrected using the CytofRUV and cyCombine algorithms for the Trussart_cytofruv dataset. Each point represents a sample. B Distribution of CD14, CD45RA, and CD11c expression for uncorrected, CytofRUV-, and cyCombine-corrected supercells for Trussart_cytofRUV dataset. C Scores for metrics used to assess the preservation of biological signals of cyCombine and CytofRUV. ARI and NMI were only calculated for corrected supercells, as these metrics require a comparison with respect to the uncorrected supercells