klionsing.blogg.se - Storm in a teacup czerski

Hi again Kevin, and thank you for your patiente. So, to sum up, i think the error is that i do not know what do i have to type in the field Name and gene_symbol from this line: modGenes = annot$Name In my dataExprhigado the head is this gene_symbol H1.1Īnd in the annotation file is: 0 WormBase_imported gene 6894 7124. I have a doubt about what to write in "Name" and "gene_symbol" fields. So, i think the error is here modGenes = annot$Name Then it outputs me txt files, in both i see the column AltName says n/a, then i saw this str(modGenes) TRUE, threshold = 0, nodeNames = modProbes, altNodeNames = ".txt", sep=""), nodeFile = paste("CytoscapeInput-nodes-", Paste("CytoscapeInput-edges-", paste(module, collapse="-"), ModGenes = annot$Nameĭimnames(modTOM) = list(modProbes, modProbes)Ĭyt = exportNetworkToCytoscape(modTOM, edgeFile = InModule = is.finite(match(moduleColorsHigado, module)) TOM = TOMsimilarityFromExpr(datExprhigado, power = 18) Hi everyone, i changed my script like this: module = "black" Hoy may i solve it? is there anyway to correct this? Its says basically that the objetc nodeNames do not have content.and the adjMat no not have dimnames.

+ nodeAttr = moduleColorsAutomatic)Įrror in exportNetworkToCytoscape(modTOM, edgeFile = paste("CytoscapeInput-edges-", :Ĭannot determine node names: nodeNames is NULL and adjMat has no dimnames. + nodeFile = paste("CytoscapeInput-nodes-", paste(modules, collapse="-"), ".txt", sep=""), + edgeFile = paste("CytoscapeInput-edges-", paste(modules, collapse="-"), ".txt", sep=""),

> dimnames(modTOM) = list(modProbes, modProbes) > dimnames(modTOM) = list(modProbes, modProbes) > library(WGCNA)

> inModule = is.finite(match(moduleColorsAutomatic, modules)) > annot = read.csv(file = "anotacionEG.csv") > TOM = TOMsimilarityFromExpr(datExprhigado, power = 18) > lnames = load(file = "modulePreservation.RData") > ADJ1=abs(cor(datExprhigado,use="p"))^6 Hello, im new in RNA-Seq World, and im trying to export a network from WCGNA to Cytoscape, im trying this command (and the output is here too) > library(WGCNA)