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I'm working with R using the Seurat package on mac.

The data I downloaded is on GEO and the file is - GSE93374_Merged_all_020816_BatchCorrected_LNtransformed_doubletsremoved_Data.txt.gz

I guess the file I've downloaded is too big because after trying to normalize the data using Seurat, I received the following error code:

Error: vector memory exhausted (limit reached?)

I followed the thread on Stack Overflow but it didn't help. My machine has 16GB, and I guess that's why, according to the "NOTE" on the answer, it wasn't helpful.

What can I do? Maybe try and minimize the size of the text file?

Thanks

Mika Li
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  • You have to show which commands exactly you used for reading-in the count file. Because 16GB is not bad actually ... Can you show us the exact code from reading-in until occurrence of error? - I see when you try to normalize that data - how did you normalize? – Gwang-Jin Kim Dec 12 '21 at 08:47
  • I see that GSE file is less than half GB in size - so Seurat - using sparse matrix - should be able to deal with it. – Gwang-Jin Kim Dec 12 '21 at 08:49
  • This guy had same error on a Mac with 16GB RAM 64 bit - https://stackoverflow.com/questions/51295402/r-on-macos-error-vector-memory-exhausted-limit-reached - His solution was: open in home the `~/.Renviron` file - if not existing, create. then write into `R_MAX_VSIZE=100Gb` - instead manually creating the site, one can use the `usethis` package and do `usethis::edit_r_environ()` which opens dialog where you set the variable. Some other guy, in addition deleted all other files containing memory-consuming variables using `rm(someObject1, someObject2, ...)` which freed memory in addition. – Gwang-Jin Kim Dec 12 '21 at 08:58
  • @Gwang-JinKim Thanks' but I've tried this guy's solution and it didn't work. I added to my question the reference to that thread on StackOverflow. – Mika Li Dec 13 '21 at 15:07
  • but your machine is 64bit or 32bit? – Gwang-Jin Kim Dec 13 '21 at 18:02
  • @Gwang-JinKim 64-bit – Mika Li Dec 15 '21 at 16:03

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