Error in WGCNA?

Question

[harshraje19]

Hi Friends,

I am performing WGCNA in R. I am getting following error messages. Can anyone help me out to solve this error? Thanks

> dissTOM = 1-TOM
Error: vector memory exhausted (limit reached?)
> dissTOM = 1-TOM
Error: vector memory exhausted (limit reached?)
> dissTOM = 1-TOM
Error: vector memory exhausted (limit reached?)
> dissTOM = 1-TOM
Error: vector memory exhausted (limit reached?)
> geneTree = hclust(as.dist(TOM), method = "average");
Error: vector memory exhausted (limit reached?)
> geneTree = hclust(as.dist(TOM), method = "average");
Error: vector memory exhausted (limit reached?)
> geneTree = hclust(as.dist(TOM), method = "average");
Error: vector memory exhausted (limit reached?)
> save.image("~/Desktop/Ambika_WGCNA/WGCNA_step2.RData")
Error: Unable to establish connection with R session

> geneTree = hclust(as.dist(TOM), method = "average");
Error: vector memory exhausted (limit reached?)

Answer 1

[Kevin Blighe]

You need a greater allocation of RAM / 'memory'. If you cannot allocate more RAM, try to reduce the input number of variables by removing low expressed genes and those with low variance.

Edit: your very first command could be due to another issue. Try to simply restart your computer in order to clear your cache. When you start a new analysis in R, always start a new R session.

Kevin