Memory allocation code while running Seurat ?
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2.0 years ago

I ran the code as given on the PBMC data (https://satijalab.org/seurat/articles/pbmc3k_tutorial.html) designed by your respected Satija lab.

However when I run the code my dataset it shows an error stating "cannot allocate vector of size 20.7 Gb".

However, when I set the memory limit to maximum using the command memory.limit(), it again states an error message "memory.limit() is no longer supported"

Is it due to the size of my matrix file as there are a comparably large number of cells (i.e., 29733 x 100064) in my data unlike the PBMC data?

I'm a beginner in R and would be really grateful if you could please assist me with this issue. I have attached the screenshot of my data matrix size as shown in R console.

enter image description here

Single cell analysis • 1.7k views
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I have following specs:

Processor: Intel Xeon RAM: 64 GB Storage: 1 TB HDD

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To help troubleshoot, please provide the specific step in your code that produces the error. And yes, it does look like memory.limit is deprecated in R, the following may be helpful https://rdrr.io/r/base/Memory-limits.html

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