An end-to-end Single-Cell Pipeline designed to facilitate comprehensive analysis and exploration of single-cell data.
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Error: Cannot find assay 'SCT' in this Seurat object ? #214
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xflicsu opened 7 months ago
I use Integration_SCP with SCT and Harmony to normalize and remove betch effect as follow commond:
sce <- Integration_SCP(srtMerge = alldata, batch = "orig.ident", integration_method = "Harmony",linear_reduction_dims_use = 1:50,nonlinear_reduction = "umap",vars_to_regress="percent.mito",normalization_method="SCT")
And I catch the following error:
Non-linear dimensionality reduction(umap) using Reduction(Harmony, dims:1-50) as input Error: Cannot find assay 'SCT' in this Seurat object
So, how to fix the error? Thanks!