Comments (2)
hi @sokratiag
Thank you for your interest on SPOTlight.
As you can see in the documentation of the parameters x and y represent the single-cell and mixture dataset, respectively. Can be a numeric matrix, SingleCellExperiment or SeuratObjecy. Therefore, I would suggest to convert st_count to a matrix format and it shouldn't return any errors
Sorry for the confusing error message, it was a copy-paste mistake and should now be fixed in the main branch on GitHub.
Please let me know if you encounter any further issues!
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hi @MarcElosua
Thanks a lot for your help - I converted the data frame to a matrix and problem solved!
from spotlight.
Related Issues (20)
- Issues using plotSpatialScatterpie() with Seurat HOT 2
- Assay Parameter not working in SPOTlight function HOT 2
- error when using trainNMF function HOT 3
- Seurat Object Issues
- Issue plotSpatialScatterpie with a seurat object HOT 2
- Questions about the workflow of SPOTlight HOT 5
- Question about SPOTlight_deconvolution_analysis HOT 7
- Question about accessing older versions of SPOTlight HOT 4
- problem with plotTopicProfiles: Error in plotTopicProfiles(x = mod, y = sce$Cell_Type, facet = FALSE, : is(x, "NMFfit") is not TRUE HOT 3
- deconvolution with the same reference HOT 7
- Issue plotSpatialScatterpie with a SpatialExperiment object HOT 3
- Deconvolution cannot identify tumor cell type in tumor spatial data HOT 2
- Suspected incorrect variable names used in vignette HOT 1
- Problem on spotlight_deconvolution(old version) HOT 1
- SPOTlight function crashes R studio session HOT 4
- Convert mgs to data.frame HOT 1
- export SPOTlight results to 10x Genomics Loupe Browser HOT 3
- colData(sc_data)$subclass HOT 1
- Difference between cell type correlation and cell communication HOT 1
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