Question: Load Count Matrix
0
gravatar for Bios
14 months ago by
Bios10
Bios10 wrote:

Hi,

I'm following this tutorial here: https://satijalab.org/seurat/v3.0/pbmc3k_tutorial.html

I am getting an error when I use CreateSeuratObject. Is there something I should do when I'm loading in the data?

stemcells.data <- load(file = "/Users/Downloads/kowalcyzk_gene_counts")
stemcells <- CreateSeuratObject(raw.data = stemcells.data, min.cells = 3, min.genes = 200, project = "STEM")

Error in base::colSums(x, na.rm = na.rm, dims = dims, ...) : 
  'x' must be an array of at least two dimensions

Thanks

R • 842 views
ADD COMMENTlink modified 10 months ago by Biostar ♦♦ 20 • written 14 months ago by Bios10
2

load is a function in R to reload a saved (.Rdata) Dataset. It is not similar as read.table or read.csv. If this saved dataset contains the counts, it is under a different name than stemcell.data. So check with ls() what you all have loaded into your R session, see if you can find a counts object somewhere, or show us what ls() gives you.

stemcells.data <- load(file = "/Users/Downloads/kowalcyzk_gene_counts")

ls()
ADD REPLYlink modified 13 months ago • written 13 months ago by Benn8.0k
1

I highly doubt that "/Users/kellychau/Downloads/kowalcyzk_gene_counts" is your counts... it looks like a directory.

ADD REPLYlink written 14 months ago by benformatics1.9k

Output of head(stemcells.data)?

By the way, I noticed that three of your previous question were deleted after receiving answers. Did you do that? If so, it is bad practice and disrespectful towards the commentators. I reopened all of them. Please stop doing that or we might eventually consider suspending your account. If it was not you then please do not feel offended and simply ignore my comment.

ADD REPLYlink modified 10 months ago • written 14 months ago by ATpoint38k
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: 1384 users visited in the last hour