WGCNA: Error plotting TOM

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6.7 years ago

chetana ▴ 60

Hi everyone,

I've been working with micro array gene expression data and have been using WGCNA to get the co-expression network analysis. I'm working with 28K genes with their expression data across 36 samples. When I'm trying to plot TOM from just the expression data I get an error which I'm not sure how to fix.

Here is the error I'm getting:

Error in structure(r, class = "dendrogram") : node stack overflow Calls: TOMplot ... rev.dendrogram -> rev -> [[ -> [[.dendrogram -> structure Execution halted Error in (function (e) : node stack overflow

Is it because of large number of genes included in my analysis? But I do want to keep all of them and try plotting the TOM. I appreciate your help. Thanks!

WGCNA Expression R • 1.9k views

ADD COMMENT • link 6.7 years ago by chetana ▴ 60

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How much RAM do you have on your machine ?

ADD REPLY • link 6.7 years ago by GouthamAtla 12k

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It's a cluster that I'm running it on and RAM is around 160GB.

ADD REPLY • link 6.7 years ago by chetana ▴ 60

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