Why am I getting numbers instead of gene names in Seurat slot data?
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29 days ago
Audra • 0

Numbers instead of gene names are showing up here.

Why am I getting numbers instead of gene names at this step? It was working fine yesterday.

Here is how I have my Seurat object set up:

This is how I have my Seurat object set up.

Seurat slot scRNAseq data • 261 views
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In your counts table you set the first column to null, and commented out the line before that may have set the rownames to gene names. After loading the count matrix and before setting V1 to NULL, what does the count matrix look like?

counts[1:10, 1:10]

If the gene names are in the first column you need to uncomment the line that has rownames(counts) <- counts$V1 and run it before you remove that column.

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Thank you, I had commented that line out since it was 1.3 GB of data and it was taking a while on my humble laptop :)

It is working now.

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