Dharmesh D Bhuva, Chin Wee Tan, Agus Salim, Claire Marceaux, Marie A Pickering, Jinjin Chen, Malvika Kharbanda, Xinyi Jin, Ning Liu, Kristen Feher, Givanna Putri, Wayne D Tilley, Theresa E Hickey, Marie-Liesse Asselin-Labat, Belinda Phipson, Melissa J Davis
Spatial molecular data has transformed the study of disease microenvironments, though, larger datasets pose an analytics challenge prompting the direct adoption of single-cell RNA-sequencing tools including normalization methods. Here, we demonstrate that library size is associated with tissue structure and that normalizing these effects out using commonly applied scRNA-seq normalization methods will negatively affect spatial domain identification. Spatial data should not be specifically corrected for library size prior to analysis, and algorithms designed for scRNA-seq data should be adopted with caution...
April 18, 2024: Genome Biology