Using log2(TPM/10+1) values in Seurat
1
0
Entering edit mode
3.5 years ago
zizigolu ★ 4.3k

Hi

I have downloaded log2(TPM/10+1) values of 10X Malignant ascites single cell from GSE146026 as raw data is not available

Is there anyway to use this matrix and convert that to a Seurat object?

Thank you so much for any idea

10X Seurat R • 2.1k views
ADD COMMENT
1
Entering edit mode
3.5 years ago
fracarb8 ★ 1.7k

Starting with raw counts it's advised, but not required. You can pass your TPM matrix to CreateSeuratObject, but you need to skip the normalisation steps, as you already have the log counts. After that, you can procede with scaling (beware of the warnings if you want to do it) and the rest...

ADD COMMENT
0
Entering edit mode

Sorry you can help with this question please?

https://bioinformatics.stackexchange.com/questions/15948/making-seurat-object-from-a-processed-file

I want to make Seurat object having all of cell barcodes, genes, patients ID but I really can not find the answer

ADD REPLY
1
Entering edit mode

Read10X reads 10x output folders, and it requires the content to be exactly what it is supposed to be output by cellranger (i.e. the triad of files features, barcodes, matrix). If you are providing your own matrix you need to CreateSeuratObject(counts = yourMatrix). Just make sure that you have genes and cellsID as rownames and colnames.

ADD REPLY

Login before adding your answer.

Traffic: 1986 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6