Hi all,

I'm trying out a preservation analysis in WGCNA. I constructed modules from two different treatments (same genes, different samples) and now want to compare the modules. But, I'm running into this error with R version 4.0.0. I had the same error when importing the RData of module colors from previous network analyses:

# Expression data files for two treatments
# columns = genes, rows = samples
multiExpr = multiData(Set1 = datExprHot, Set2 = datExprCold)

# Input module files
# one column for geneID, one for assigned module
Hotmodule=read.csv("PTR_hot_modulelist.csv", header=TRUE) 
Coldmodule=read.csv("PTR_cold_modulelist.csv", header=TRUE) 

# Create list holding module labels for each set
colorList = list(Set1 = Hotmodule, Set2 = Coldmodule)

# Calculate module preservation statistics
system.time( {
  mp = modulePreservation(multiExpr, colorList,
                          referenceNetworks = c(1:2),
                          loadPermutedStatistics = FALSE,
                          networkType = "signed hybrid",
                          nPermutations = 200,
                          verbose = 3)
} );

Error in modulePreservation(multiExpr, colorList, referenceNetworks = c(1:2),  : 
  Color vector for set 1 does not have the correct number of entries. 
Timing stopped at: 0.033 0.008 0.04