Hi, I am trying to run the clusterRepro function (see below) but am running into a problem.

impExpr = list();
for (set in 1:nSets)
{
  impExpr[[set]] = list(data = t(impute.knn(t(multiExpr[[set]]$data))$data));
}

impExpr
eigengenes = list();
for (set in 1:nSets)
{
  eigengenes[[set]] = multiSetMEs(impExpr, universalColors = colorList[[set]], excludeGrey = TRUE);
  for (ss in 1:nSets)
  {
    rownames(eigengenes[[set]][[ss]]$data) = rownames(multiExpr[[ss]]$data);
  }
}

rownames(multiExpr[[ss]]$data)

library(clusterRepro)
cr = list();
set.seed(20);
for (ref in 1:nSets)
{
  cr[[ref]] = list();
  for (test in 1:nSets)
  {
    printFlush(system.time({
      cr[[ref]][[test]] = clusterRepro(Centroids = as.matrix(eigengenes[[ref]][[test]]$data),
                                       New.data = as.matrix(impExpr[[test]]$data),
                                       Number.of.permutations = 10000); }));
    collectGarbage();
  }
}

When I run this code I get the error message "Error in cor(Data, Centroids, use = "pairwise.complete.obs", method = "pearson") : 'x' is empty", and the website for the module preservation is down so I am unsure of how to proceed.

Both WGCNA and clusterRepro are CRAN packages, not Bioconductor. You can ask over at biostars.org, or on r-help@r-project.org.