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Load Count Matrix

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
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updated by Biostar Biostar • written by Bios • Bios

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.

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written by ATpoint ATpoint

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

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written by benformatics benformatics

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()
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written by Benn Benn

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