Could not find count matrix in specified seurat object

[yanglq-bioinfo]

Hi,
I extracted count matrix and coord from my seurat object, the format as:

coords_df
barcodes x y
AAACAAGTATCTCCCA-1_B56_H1 AAACAAGTATCTCCCA-1_B56_H1 8868 7568
AAACACCAATAACTGC-1_B56_H1 AAACACCAATAACTGC-1_B56_H1 2698 8727
AAACAGTGTTCCTGGG-1_B56_H1 AAACAGTGTTCCTGGG-1_B56_H1 4480 10539
AAACATTTCCCGGATT-1_B56_H1 AAACATTTCCCGGATT-1_B56_H1 8496 8990

count_mtr
AAACAAGTATCTCCCA-1_B56_H1 AAACACCAATAACTGC-1_B56_H1
C2orf68 0 0
C4orf19 0 20
C4orf54 12 0

Now,I running this code
spata_obj <- initiateSpataObject_CountMtr( coords_df, count_mtr, sample_name='H1', image = NULL, SCTransform = TRUE, NormalizeData = list(normalization.method = "LogNormalize", scale.factor = 3000), FindVariableFeatures = list(selection.method = "vst", nfeatures = 3000), ScaleData = TRUE, RunPCA = list(npcs = 30), FindNeighbors = list(dims = 1:30), FindClusters = list(resolution = 0.8), RunTSNE = TRUE, RunUMAP = list(dims = 1:30), verbose = TRUE )

but I got this error:
Error in value[3L] :
Could not find count matrix in specified seurat object. Did you choose the correct method?
Calls: initiateSpataObject_CountMtr ... tryCatchList -> tryCatchOne -> ->

I don't know how to change it

[renyzh5]

I meet the same problem, need help, too.

[zyfvae514]

I also met this issue. The details of error log is:
Error in value[3L] :
Could not find count matrix in specified seurat object. Did you choose the correct method?

[kueckelj]

Dear all, I am sorry for the late reply. The last version release has been quite time and energy consuming and our team is small. We have adjusted the asSPATA2() function to work with the new Seurat v5. The tutorial on package compatibility elaborates on that. I hope that this fixes any problems. If you still encounter some with the function asSPATA2() please let us know. We will be able to fix these things faster from now on.