Question: Module preservation WGCNA
gravatar for bekah
11 days ago by
bekah20 wrote:


I have a single network that I have created using WGCNA, is it possible to test module preservation on just the one network. I tried using the following:


data=read.csv("preservation.csv", header=TRUE) # expression data file, with columns = genes and rows = samples

moduledata=read.csv("modulelist.csv", header=TRUE) # module file, with two columns, one for geneID and one for assigned module
colorsmodule = moduledata$Module

multiExpr=data #this is the expression data
colorList = colorsmodule # this is the list of modules

system.time( {
  mp = modulePreservation(multiExpr, colorList, referenceNetworks=1,
                          nPermutations = 1000,
                          networkType = "signed",
                          randomSeed = 2905,
                          verbose = 4, 
                          indent = 0)

but it gave the error:

Error in multiExpr[[set]]$data : $ operator is invalid for atomic vectors
Timing stopped at: 2.15 0 2.17 

Which I assume is because it is looking for two sets to compare? Should I just subset my data to say just 5 samples and input this? Or is it just not possible to test for robustness in this case?

Best wishes,


ADD COMMENTlink modified 11 days ago by Peter Langfelder1.6k • written 11 days ago by bekah20
gravatar for Peter Langfelder
11 days ago by
United States
Peter Langfelder1.6k wrote:

Create a multi-data structure with two copies of your data, perhaps like this:

multiExpr = multiData(Set1 = data, Set2 = data)
colorList = list(Set1 = colorsmodule)

Then run modulePreservation with this input and look at module quality scores in the output (ignore the preservation metrics).


ADD COMMENTlink written 11 days ago by Peter Langfelder1.6k

Hi, sorry for the delay in responding I have just moved house! Thank you very much, I will try this ASAP!

ADD REPLYlink written 5 days ago by bekah20
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