Comments (3)
MarcElosua
commented on August 17, 2024
Hi @williamsdrake,
Thank you very much for your interest in SPOTlight and your thorough debugging already!
One thing I think could be worth checking is if the slot counts is present in spe. If that doesn't work, you can also pass directly the count matrices to x & y which would circumvent the need to call .extract_counts.
Let me know if this helps!
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carlosccfraga
commented on August 17, 2024
I am having the same problem. I did everything I could and didnt work. Please check it.
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HelenaLC
commented on August 17, 2024
Could u print both the single call and spatial data object?
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Related Issues (20)
- 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
- SPOTlight with low numbers of genes per spot HOT 1
- Does the new version of SPOTlight no longer support data from Seurat? HOT 1
- ERROR: dependency ‘arrangements’ is not available for package ‘SPOTlight’ HOT 4
- test_spot_fun HOT 2
- Error in trainNMF(x = x, y = y, groups = groups, mgs = mgs, n_top = n_top, : ids %in% names(mgs) are not TRUE
- Parallel run HOT 2
- function plotSpatialScatterpie with image=TRUE does not work HOT 6
- plotInteractions HOT 8
- What does the 'decon_df' mean? HOT 5
- Error in .extract_counts(y, assay, slot) : !is.null(colnames(x)) is not TRUE HOT 2
- ST technology (the predecessor of 10X Visium technology) HOT 1
- Error in `SeuratObject::GetAssayData()`: HOT 4
- plotSpatialScatterpie HOT 9
- assay %in% SeuratObject::Assays(x) is not TRUE HOT 1
- Q - Visium analysis - subset image and spot demultiplexing HOT 5
- packages version HOT 3
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