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
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?
2 answers
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)
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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.