Question: Load Count Matrix
0
gravatar for Bios
3 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 • 196 views
ADD COMMENTlink modified 12 weeks ago • written 3 months ago by Bios10
1

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

ADD REPLYlink written 3 months ago by benformatics1.1k
1

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 12 weeks ago • written 12 weeks ago by Benn7.8k

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 consider suspending your account. If it was not you then please do not feel offended and simply ignore my comment.

ADD REPLYlink written 3 months ago by ATpoint24k
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