substance BxH

Question

[samalkawijeweera]

what is substance BxH in WGCNA annotations file?how to get it?

[Kevin Blighe]

Seems to available here? https://horvath.genetics.ucla.edu/html/CoexpressionNetwork/DifferentialNetworkAnalysis/

Which tutorial are you following?

[samalkawijeweera]

Hi Kevin It's https://horvath.genetics.ucla.edu/html/CoexpressionNetwork/Rpackages/WGCNA/Tutorials/

"Network analysis of liver expression data from female mice: finding modules related to body weight " Thank you

[Kevin Blighe]

Great, so, BxH is a strain of mouse

[samalkawijeweera]

I am using the folllowing code for network export in WGCNA to Cys. It doesn't assign the nodes and edges properly. there is some error with code that I cannot figureout Could you please have a look Thank you veyr much

colors = read.csv("organelleCOLturnprots.csv")
colors = as.vector(colors)
controlData = read.csv("control.csv", header = TRUE, row.names = 1)
saltData = read.csv("salt.csv", header = TRUE, row.names = 1)

# Recalculate topological overlap if needed
controlTOM = TOMsimilarityFromExpr(controlData, power = 6);
saltTOM = TOMsimilarityFromExpr(saltData, power = 6);
# Select modules
modules = c("black");
# Select module probes
probes = names(controlData)
#inModule = is.finite(match(colors, modules));
inModule = (colors==modules)
modProbes = probes[inModule];
probes = c("TraesCS7B01G148000.1",
"TraesCS3B01G299300.1","TraesCS6B01G342400.1","TraesCS6D01G291600.1",
"TraesCS6D01G291600.2"," TraesCS3A01G250200.1","TraesCS3B01G279700.1",
" TraesCS3D01G250600.1","TraesCS2A01G467900.1"," TraesCS2B01G490900.1",
"TraesCS2A01G250800.1","TraesCS2D01G467700.1","TraesCS5D01G432900.1",
"TraesCS3D01G160800.1","TraesCS4B01G324200.1","TraesCS5A01G496700.1","TraesCS6D01G001700.1")

modGenes = annot$Gene_symbol [match(modProbes, annot$substanceBxH)];


# Select the corresponding Topological Overlap
modTOMSalt = saltTOM[inModule, inModule];
dimnames(modTOMSalt) = list(modProbes, modProbes)

modTOMControl = controlTOM[inModule, inModule];
dimnames(modTOMControl) = list(modProbes, modProbes)
# Export the network into edge and node list files Cytoscape can read

cytSalt = exportNetworkToCytoscape(saltTOM,
                                   edgeFile = "Saltedges.txt",
                                   nodeFile = "Saltnodes.txt",
                                   weighted = TRUE,
                                   threshold = 0.2,
                                   nodeNames = colnames(colours))
cytControl = exportNetworkToCytoscape(controlTOM,
                                      edgeFile = "Controledges.txt",
                                      nodeFile = "Controlnodes.txt",
                                      weighted = TRUE,
                                      threshold = 0.2,
                                      nodeNames = colnames(colours))

cytexpSalt = cytSalt$edgeData
cytexpControl = cytControl$edgeData
write.csv(cytexpSalt, "outputSalt.csv")
write.csv(cytexpControl, "outputControl.csv")
View(cytControl)

[Kevin Blighe]

Hi, well, I cannot see any error message, so, I cannot help you right now. What I mean is that you have posted a lot of code, but you have not explained which part produces the error, nor have you shown what is the error message.