CreateSeuratObject error: No cell names (colnames) names present in the input matrix

[derrik-gratz]

Problem:

When trying to a dataset from my lab, I am unable to create the seurat object. I get the following errors:

> obj <- Read10X_h5(here('raw_feature_bc_matrix.h5'))
Genome matrix has multiple modalities, returning a list of matrices for this genome
> obj <- CreateSeuratObject(obj)
Error in CreateAssayObject(counts = counts, min.cells = min.cells, min.features = min.features,  : 
No cell names (colnames) names present in the input matrix

[derrik-gratz]

This is likely due to multiple assays being present in the cellranger output, such as a cite-seq panel. We will discuss how to load and use that data in a later lecture. The CreateSeuratObject() function expects only one matrix for one assay: gene expression. The Read10X_h5 function probably returned a list of matrices, so you should specify the gene expression matrix in the CreateSeuratObject call. You can read up on the Seurat function CreateAssayObject for how to provide additional assays to your object.

[derrik-gratz]

e.g.

> obj <- CreateSeuratObject(obj[["Gene Expression"]])