WGCNA modulePreservation Error

Question

[abnerapsley]

Hi all,

I have been using WGCNA to identify gene coexpression modules for two different data sets. I now want to use the modulePreservation function to test if the modules are preserved from one data set to the other. I have expression matrices for both sets of data, and module assignments (colors) for the first set of data in the required structure. I have also used the goodGenesSamples function in WGCNA to filter out any genes that have low variances across my samples. I run the following command, where multiExpr is a list of my coexpression matrices and multiColor is a list of module assignments for my first expression matrix:

mp = modulePreservation(multiExpr, 
                          multiColor,
                          referenceNetworks = 1,
                          nPermutations = 200,
                          randomSeed = 1,
                          quickCor = 0,
                          verbose = 5)

And get the following error:

Error in .checkExpr(multiData, verbose, indent): The submitted 'multiExpr' data contain genes or samples with zero variance or excessive counts of missing entries. Please use the function goodSamplesGenes on each set to identify the problematic genes and samples, and remove them before running modulePreservation.

I am not sure why I would get this error because I have already filtered out low-variance genes withe the goodGenesSamples function and have no missing values in the expression matrices. I also tried to filter out the genes in both datasets that fall under the median value of variance across all genes. This was to see if the previous command was not stringent enough in its filtering.

Have any of you had similar errors with this type of analysis? If so, any thoughts on next steps I can take? Thanks!

[andres.firrincieli]

can you run again

gsg = goodSamplesGenesMS(multiExpr, verbose = 3);
gsg$allOK

[abnerapsley]

This worked perfectly! I had to go through each dataset individually in the "multiExpr" list and then replace them in the list. Thank you for the help!