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I am using Seurat v.4.0.3 to analyze some Visum spatial expression data. I run the following commands:
seurat.obj <- SCTransform(seurat.obj, assay = "Spatial", verbose = FALSE) seurat.obj <- FindSpatiallyVariableFeatures(seurat.obj, assay = "SCT", selection.method = "markvariogram")
And get the following error:
Error in h(simpleError(msg, call)) : error in evaluating the argument 'x' in selecting a method for function 'as.matrix': subscript out of bounds
The error does not occur if I subset features only variable features:
sce <- FindSpatiallyVariableFeatures(sce, assay = "SCT", features = VariableFeatures(sce), selection.method = "markvariogram")
Is it intended that you can only look for spatially variable genes within HVGs?
The text was updated successfully, but these errors were encountered:
See #4611
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I am using Seurat v.4.0.3 to analyze some Visum spatial expression data. I run the following commands:
And get the following error:
The error does not occur if I subset features only variable features:
Is it intended that you can only look for spatially variable genes within HVGs?
The text was updated successfully, but these errors were encountered: