Error while running FindTransferAnchors on Seurat V5

[melodyyazdi]

Hi! I am trying to run FindTransferAnchors on my single cell object(day14og) and my spatial object(day14controlspatial). It keeps on giving the following error;

< anchors <- FindTransferAnchors(reference = day14og, query = day14controlspatial) 
Performing PCA on the provided reference using 12 features as input.
Warning in irlba(A = t(x = object), nv = npcs, ...) :
  You're computing too large a percentage of total singular values, use a standard svd instead.
Warning in irlba(A = t(x = object), nv = npcs, ...) :
  did not converge--results might be invalid!; try increasing work or maxit
Projecting cell embeddings
Error in (function (cond)  : 
  error in evaluating the argument 'x' in selecting a method for function 't': subscript out of bounds >

I ran the following commands before running the FindTransferAnchors.

day14og <- CreateSeuratObject(counts = day14og, project = "day14original")
day14og <- NormalizeData(day14og, normalization.method = "LogNormalize")
day14og <- FindVariableFeatures(day14og, selection.method = "vst", nfeatures = 2000)
all.genes <- rownames(day14og)
day14og <- ScaleData(day14og, features = all.genes)
day14og <- RunPCA(day14og)
day14og <- FindNeighbors(day14og, dims = 1:30)
day14og <- FindClusters(day14og, resolution = 0.5)
day14og <- RunUMAP(day14og, dims = 1:30)

#spatial 
day14controlspatial <- Load10X_Spatial('day14spatial',
                                       filename = `"sampleb2filtered_feature_bc_matrix.h5",`
                                       assay = "Spatial",
                                       slice = "slice1",
                                       filter.matrix = TRUE,
                                       to.upper = FALSE,
                                       image = NULL,)
day14controlspatial <- NormalizeData(day14controlspatial, normalization.method = "LogNormalize")
day14controlspatial <- FindVariableFeatures(day14controlspatial, selection.method = "vst", nfeatures = 2000)
all.genesspatial <- rownames(day14controlspatial)
day14controlspatial <- ScaleData(day14controlspatial, features = all.genesspatial)
day14controlspatial <- RunPCA(day14controlspatial)
day14controlspatial <- FindNeighbors(day14controlspatial, dims = 1:30)
day14controlspatial <- FindClusters(day14controlspatial, resolution = 0.5)
day14controlspatial <- RunUMAP(day14controlspatial, dims = 1:30)

I have been stuck on this problem for some time. Any help would be greatly appreciated. Thank you!

[igrabski]

Hi, can you show the outputs if you just run day14og and day14controlspatial? The error message shows that you have 12 features in your reference, which seems odd.

[dcollins15]

Hi @melodyyazdi ,

Thank you for reaching out! We’re always grateful when folks take the time to help make Seurat better 🙂

Unfortunately, with the details provided, we cannot reproduce your issue. To help us better understand and resolve this issue, please ensure that you provide the following information when reporting a bug:

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We’re going to go ahead and close this issue for now, but once you’ve gathered these details, we strongly encourage you repost and we will be more than happy to help you resolve the problem.