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Description
Thank you for developing such a powerful tool—BayesSpace!!
I encountered a runtime error and would like to ask for help.
I'm working with BGI's Stereo-seq data, stored as a Seurat .rds file. Based on previous suggestions, I converted the Seurat object into a SingleCellExperiment format. However, when running the following step:
sce = spatialCluster(sce, nrep = 1000, burn.in = 100, q = 10)
but get error: “Error: subscript contains invalid names” . I wonder if this issue is related to the data structure. Could you please advise on how to resolve this error?
Below is the full code I used:
library(Seurat)
library(SeuratData)
library(BayesSpace)
library(tidyverse)
seurat = readRDS("LP3_cluster.rds") # load Seurat data
seurat = Seurat::FindVariableFeatures(seurat)
seurat = Seurat::ScaleData(seurat)
seurat = Seurat::RunPCA(seurat)
Convert to SCE
diet.seurat = Seurat::DietSeurat(seurat, graphs = "pca")
sce = as.SingleCellExperiment(diet.seurat)
colData(sce) = cbind(colData(sce), seurat@images$st@coordinates)
BayesSpace Workflow
sce = spatialPreprocess(sce, platform = "Visium", skip.PCA = TRUE, log.normalize = FALSE)
sce = spatialCluster(sce, nrep = 1000, burn.in = 100, q = 10)