Memory allocation error

Question

[Azhar]

HI I am runnig WGCNA code for calculating co expression adjacency Matrix but I am getting this error I am running this scrip in C directory and it has 60 Gb free space so why it still gives this error

> coexpression<-adjacency(data)
Error: cannot allocate vector of size 28.7 Gb
In addition: Warning messages:
1: In cor(datExpr, use = "p") :
  Reached total allocation of 3810Mb: see help(memory.size)
2: In cor(datExpr, use = "p") :

[andrew.j.skelton73]

The 3810Mb limit it's referring to is RAM, not disk space.

[Azhar]

Thanks andrew but what is the mean of

cannot allocate vector size 28.7 Gb

[WouterDeCoster]

Hello Azhar!

It appears that your post has been cross-posted to another site: https://support.bioconductor.org/p/93818/

This is typically not recommended as it runs the risk of annoying people in both communities.

Answer 1

[Jean-Karim Heriche]

To be more explicit, it seems you're using a computer with only 4Gb of RAM but your data requires 29 Gb so try running your analysis on a computer with 32 Gb of RAM. Note that if you're using a 32bit version of Windows, you can only use at most 4 Gb even if the computer has more.