Question: bulk analysis by seurat
0
gravatar for ayatrience
13 months ago by
ayatrience0
ayatrience0 wrote:

Because seurat package is also technically available for bulk RNA-seq analysis and very easy to analyze for my bulk data with several conditions, I am trying to use Seurat for bulk analysis currently.

I use TPM countdata (rows are genes and cols are sample name) for CreateSeuratObject but gene names didn't appear in seurat object as features.

What kind of input is appropriate for making seurat object?

I have TPM count data and gene names in CSV format.

rna-seq seurat name gene • 1.0k views
ADD COMMENTlink modified 13 months ago • written 13 months ago by ayatrience0
1

For questions like this, you really need to show all code that you have used, and paste a sample of your data.

ADD REPLYlink modified 13 months ago • written 13 months ago by Kevin Blighe66k

Thank you for teaching. I did like below.

bulk <- CreateSeuratObject(counts=TPM, assay = "RNA")

TPM is the list that contains the count data showed in TPM and the rows are genesID and cols are sample name.

ADD REPLYlink written 13 months ago by ayatrience0

I see - you likely need to use the meta.data parameter, too.

ADD REPLYlink written 13 months ago by Kevin Blighe66k

Can you show more of your code and the first lines of your input ?

ADD REPLYlink written 12 months ago by nlehmann100
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 2091 users visited in the last hour