Error in convertToSeurat function, "Error in FUN(left, right) : non-numeric argument to binary operator"

[maki8080]

Error in convertToSeurat function, "Error in FUN(left, right) : non-numeric argument to binary operator"

[maki8080]

Hi,
The reason for the error may have been that image.seurat@coordinates obtained by input in the Read10X_Image function was character. I converted it to numeric.

``
object.new <- CreateSeuratObject(assay(decont_obj), assay = "Spatial")
image.seurat <- Read10X_Image(image.dir = "B1_SRT/image", filter.matrix = T)
image.seurat@coordinates$imagerow <- as.numeric(image.seurat@coordinates$imagerow)
image.seurat@coordinates$imagecol <- as.numeric(image.seurat@coordinates$imagecol)
ts_coord <- GetTissueCoordinates(image.seurat)

nrow(ts_coord) == ncol(object.new) # TRUE
image.seurat <- image.seurat[Cells(x = object.new)]
DefaultAssay(object = image.seurat) <- "Spatial"
object.new[["slice1"]] <- image.seurat
object.new

``
Is it OK to proceed with the downstream analysis with the seurat object obtained this way?

Thanks!

Maki

[zijianni]

Thanks for identifying the issue! Yes, you can directly export the decontaminated expression matrix from SpotClean into Seurat in different ways.