Comments (4)
Hi @galaxyeee,
Thank you for your interest in SPOTlight! Have you tried installing the package arrangements
? It seems like it is an unmet dependency!
Best,
Marc
from spotlight.
Hi @MarcElosua ,
Thank you very much for your kind reply. This issue has been resolved.
However, the error was not resolved during troubleshooting, so I asked again.
This error occurred during the creation of "mgs_df".
genes <- !grepl(pattern = "^Rp[l|s]|Mt", x = rownames(brca.sce))
I converted the single cell seurat object as a reference into a SingleCellExperiment object and used that data to save the "genes".
mgs <- scoreMarkers(brca.sce, subset.row = genes)
After going through the scoremarkers function, this error occurred.
Error in FUN(x, table, nomatch = nomatch, incomparables = incomparables) :
'match' requires vector arguments
5. FUN(x, table, nomatch = nomatch, incomparables = incomparables)
4. match(desired.comparisons, averaged.comparisons)
3. match(desired.comparisons, averaged.comparisons)
2. .cross_reference_to_desired(pre.ave$averaged.comparisons, desired.comparisons, collapse.symmetric = collapse.symmetric)
1. scoreMarkers(brca.sce, row.data = genes, groups = brca.sce$celltype_major)
Or when using SPOTlight function, I wonder if I can just put the markerlist data frame in parameter "mgs" and use other values than "mean.AUC" in "weight_id".
I would really appreciate it if you let me know if there is a solution. Thank you!
Best,
EUNHA
from spotlight.
Hi @galaxyeee
Have you set the colLabels(sce) <- factor(cluster)
or pass the groups arguments to specify the cell type groups out <- scoreMarkers(sce, groups=kout$cluster)
?
It could be the issue is there.
Best,
Marc
from spotlight.
Hi @MarcElosua
Thanks to you, I solved the error.
Thank you.
Best,
EUNHA
from spotlight.
Related Issues (20)
- export SPOTlight results to 10x Genomics Loupe Browser HOT 3
- colData(sc_data)$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
- 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
- Error slot %in% SummarizedExperiment::assayNames(x) is not TRUE HOT 3
- 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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