In a recent paper, Watanabe et al. 94 introduced a different methodology to test for cell type – complex trait association based on MAGMA. Their proposed methodology tests for a positive relationship between gene expression levels and gene-level genetic associations with a complex trait (using all genes). Their method uses the average expression of each gene in all cell types in the dataset as a covariate. We examined the method of Watanabe et al. in detail, and decided against its use for multiple reasons.
