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
Cytoscape developer here. Sorry, I can only help to narrow down the issues here. They all appear to be with functions in the WGCNA package, prior to actually working with Cytoscape. Our team is working on an R tutorial for WGCNA analysis using the RCy3 package, but it's complicated and we haven't figured it out yet either!