vector memory exhausted (limit reached?)
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10 days ago
50cf32b2 • 0

I am new to bioinformatics analysis, so please excuse my very basic question.

In my scRNA seq analysis, I tried to conduct ssGSEA analysis by using Bioconductor package escape. I followed the procedure described in https://ncborcherding.github.io/vignettes/escape_vignette.html, and have succeeded up to the point of adding the ssGSEA score to the metadata.

However, when I tried to visualize the data, the following was occurred as following;

enrichmentPlot(My data, 
               gene.set = "HALLMARK〜〜",
               gene.sets = gene.sets,
                group = "group")  + 
     scale_color_manual(values = colorblind_vector(5)[c(1,4)])


Error: vector memory exhausted (limit reached?)
asMethod(object) : 
  sparse->dense coercion: allocating vector of size 15.9 GiB

I tried to solve this problem by referring following post, but it did not work. https://stackoverflow.com/questions/51295402/r-on-macos-error-vector-memory-exhausted-limit-reached

Step 1: Open terminal,
Step 2:
cd ~
touch .Renviron
open .Renviron
Step 3: Save the following as the first line of .Renviron:
R_MAX_VSIZE=100Gb 
Step 4: Close RStudio and reopen

I would appreciate it if someone could let me know the solutions. I would be grateful for your support.

escape seurat scGSEA Rstudio. • 235 views
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It is clearly an insufficient memory error, so an obvious solution is to get (a computer with) more memory. It is difficult to be more specific without knowing the details of your computer configuration. As a general rule, each question should be accompanied by details about the operating system, RAM size, etc. You can never go wrong by providing extra information, and it avoids follow-up posts like the one I am about to conclude.

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I'm very sorry for the late reply.

Information about my current R Session is as following;

sessionInfo() R version 4.2.0 (2022-04-22) Platform: x86_64-apple-darwin17.0 (64-bit) Running under: macOS Catalina 10.15.7

In addition, information about my Seurat object is as following; 21319 features across 110524 samples within 2 assays

I'm a complete beginner in both R studio and bioinformatics analysis, so I apologize for the lack of basic knowledge.

I would appreciate it if you could let me know the solutions.

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0
Entering edit mode

What are the dimensions (genes, cells) in your Seurat object and what are your machine specs (memory)?

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0
Entering edit mode

I'm very sorry for the late reply.

Information about my current R Session is as following;

sessionInfo() R version 4.2.0 (2022-04-22) Platform: x86_64-apple-darwin17.0 (64-bit) Running under: macOS Catalina 10.15.7

In addition, information about my Seurat object is as following; 21319 features across 110524 samples within 2 assays

I'm a complete beginner in both R studio and bioinformatics analysis, so I apologize for the lack of basic knowledge.

I would appreciate it if you could let me know the solutions

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