Hello,

I have a large set of genes (~58 000) that I have analyzed using WGCNA.

now I'm trying to export a network to Cytoscape, by calculating again TOM = TOMsimilarityFromExpr(datExpr, power = 6);

This is giving me a hard time. Even if I enablethreads(), it says TOM calculation adjacency.. will not use multithreading.

And than the memory runs out.

I have tried not to calculate TOM again. This is my data:

lnames = load(file = "timecourse.RData"); lnames = load(file = "timecourse_networkConstruction-auto.RData") lnames = load(file = "timecourseTOM.RData-block.1.RData") lnames = load(file = "timecourseTOM.RData-block.2.RData")

as.matrix(TOM) TOM.mat = as.matrix(TOM)

Read in the annotation file

annot = read.csv(file = "geneannotall.csv");

Select modules

modules = c("lightcyan");

Select module probes

probes = names(datExpr) inModule = is.finite(match(moduleColors, modules)); modProbes = probes[inModule]; modGenes = annot$gene[match(modProbes, annot$OfficialGeneName)];

Select the corresponding Topological Overlap

modTOM = TOM.mat[inModule];

dimnames(modTOM) = list(modProbes)

Error in dimnames(modTOM) = list(modProbes) : 'dimnames' applied to non-array

Export the network into edge and node list files Cytoscape can read

cyt = exportNetworkToCytoscape(modTOM, edgeFile = paste("CytoscapeInput-edges-", paste(modules, collapse="-"), ".txt", sep=""), nodeFile = paste("CytoscapeInput-nodes-", paste(modules, collapse="-"), ".txt", sep=""), weighted = TRUE, threshold = 0.3, nodeNames = modProbes, altNodeNames = modGenes, nodeAttr = moduleColors[inModule]);

Error in checkAdjMat(adjMat, min = -1, max = 1) : adjacency is not square

So I get these two errors. Can anyone explain to me what the problem is?

Thanks a lot Catarina