Load10X_Spatial with multimodal data

[jchariker]

Hi, I have Visium slides with gene expression and antibody capture. When using Load10X_Spatial, I get the following error.

Genome matrix has multiple modalities, returning a list of matrices for this genome Error in CreateAssayObject(counts = counts, min.cells = min.cells, min.features = min.features, : No cell names (colnames) names present in the input matrix

Is this function designed to take multimodal data? I'm using Seurat_4.0.2 with R version 4.0.3. The function works beautifully on SpaceRanger output with only gene expression.

Thanks for your help.

[zskylarli]

Hi - not super sure since I can't view your data, but since Load10X_Spatial reads the counts matrices for the paths of all h5 files provided and loads them as an assay, I would imagine Load10X_Spatial should work as long as your antibody counts matrix has the proper colnames/cell names. Can you extract and recreate the matrix to have the right structure based on your gene expression data?

[jchariker]

Hi Zhuoyan,

After I upgraded to Seurat_5.0.1, Load10X_Spatial worked beautifully. I see the gene expression and protein assays in the Seurat object.

Thanks for your help!

Julia

From: Zhuoyan Li @.> Sent: Friday, February 16, 2024 4:53 PM To: satijalab/seurat @.> Cc: Chariker, Julia @.>; Author @.> Subject: Re: [satijalab/seurat] Load10X_Spatial with multimodal data (Issue #8454)

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Hi - not super sure since I can't view your data, but since Load10X_Spatial reads the counts matrices for the paths of all h5 files provided and loads them as an assay, I would imagine Load10X_Spatial should work as long as your antibody counts matrix has the proper colnames/cell names. Can you extract and recreate the matrix to have the right structure based on your gene expression data?

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