Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Error in FindSpatiallyVariableFeatures() #4646

Closed
edward130603 opened this issue Jun 17, 2021 · 1 comment
Closed

Error in FindSpatiallyVariableFeatures() #4646

edward130603 opened this issue Jun 17, 2021 · 1 comment
Labels
bug Something isn't working duplicate This issue or pull request already exists

Comments

@edward130603
Copy link

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?

@edward130603 edward130603 added the bug Something isn't working label Jun 17, 2021
@timoast
Copy link
Collaborator

timoast commented Jun 17, 2021

See #4611

@timoast timoast closed this as completed Jun 17, 2021
@timoast timoast added the duplicate This issue or pull request already exists label Jun 17, 2021
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
bug Something isn't working duplicate This issue or pull request already exists
Projects
None yet
Development

No branches or pull requests

2 participants