How to Create a Seurat Object from Gse Data Set?
I Know That We Can Create Seurat Object from Cell Ranger Output Files(Barcode, Features, Matrix). but I Have a Gse Single Cell Data Set in Csv Format. How Do I...
I know that we can create Seurat object from cell ranger output files(barcode, features, matrix). But I have a GSE single cell data set in csv format. How do I create a Seurat object out of that?
Thanks.
a = read.csv(<csv file >, header = TRUE)
b = t(a)
c = CreateSeuratObject(counts = b, project = "my_single_cell", min.cells = 3, min.features = 200)
Error in CreateAssayObject(counts = counts, min.cells = min.cells, min.features = min.features, :
No cell names (colnames) names present in the input matrix
dput(a[1:10, 1:10])
2.0293824672699, 0, 0, 1.67916893959045, 1.25670552253723, 0,
0, 2.35019993782043, 0), Lypla1 = c(0, 0, 0, 0, 0, 0, 0, 0, 0,
0), Gm37988 = c(0, 0, 0, 0, 0, 0, 0, 0, 0, 0), Tcea1 = c(0, 0,
0, 0, 0, 0, 0, 0, 0, 0), Atp6v1h = c(0, 0, 0, 1.69750428199768,
0, 1.25670552253723, 0, 0, 0, 0), Rb1cc1 = c(0, 0, 0, 0, 0, 0,
0, 0, 0, 0), X4732440D04Rik = c(0, 0, 0, 0, 0, 0, 0, 0, 0, 0),
Pcmtd1 = c(0, 0, 0, 0, 0, 1.25670552253723, 0, 2.10469627380371,
0, 0), Gm26901 = c(0, 0, 0, 0, 0, 0, 0, 0, 0, 0)), row.names = c("AAACCCATCTGGAAGG-WT1",
"AAACGAACAACTCGTA-WT1", "AAACGAACACAGACGA-WT1", "AAACGAATCACGAACT-WT1",
"AAACGAATCAGGGTAG-WT1", "AAACGCTAGCTGACTT-WT1", "AAACGCTTCGACCTAA-WT1",
"AAAGAACAGAATCCCT-WT1", "AAAGTCCAGAGTGACC-WT1", "AAAGTCCAGTAAACAC-WT1"
), class = "data.frame")
>
1 Answer
The original table seems to have cells on rows and genes in columns, with the cell names in the first column. To get correct rownames, try this:
a = read.csv(data.csv, row.names = 1)
b = t(a)
c = CreateSeuratObject(counts = b, project = "my_single_cell", min.cells = 3, min.features = 200)
Edit: The table seems to contain normalized expression values instead of raw counts. Seurat may not be the right tool for working with that kind of data.
Sophia analyzes international trade, startup ecosystems, retail transformation, and supply chain logistics for modern digital publications.
