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

Question

[my.kim]

I did scRNA-seq using patient PBMC, 4 biological replicates. Each PBMC was tagged with 4 different types of hashtag oligos and subjected to multiplexing. Using fastq files, cellranger multi was performed and 4 matrices were generated. Using Seurat, I imported one output matrix to R studio using Read10X as follows. Next, when I used CreateSeuratOjbect and encountered this error . My data contains two different types of information where one is gene expression and the other multiplexing capture data layout .

I think it might be due to the coexistence of two different datasets, based on the message "10X data contains more than one type and is being returned as a list containing matrices of each type." Or, If I can designate the name of the column in my dataset, Seurat may read my data.

What do you think?

[GenoMax]

Future suggestion. Copy and paste actual data (and use the option to format it correctly as indicated below) where there is code. Posting screenshots makes it hard for people to copy/try your code.

Answer 1

[Adam]

I had the exact same problem, doing the exact same experiment, haha.

Reading your question though got me to the answer.

Replace:

CreateSeuratObject(counts = HC1.data , project = "HC1")

with

CreateSeuratObject(counts = HC1.data$`Gene Expression` , project = "HC1")

(Note, Gene Expression is in quotes)

[GenoMax]

Please use the formatting bar (especially the code option) to present your post better. I've done it for you this time.

Answer 2

[Väiski]

I was also using Multiplex oligos and had this problem. Adam's suggestion worked. Thank you.