Hello, I'm using the following to attempt network creation

# Load the WGCNA package
library(WGCNA)
options(stringsAsFactors = FALSE);
enableWGCNAThreads()
load("1-data_input.Rdata")
net = blockwiseModules(datExpr, power = 6, networkType = "signed", checkMissingData = TRUE, corType="bicor",
                       TOMType = "signed", minModuleSize = 30,
                       reassignThreshold = 0, mergeCutHeight = 0.05,
                       numericLabels = TRUE,
                       pamStage = TRUE, pamRespectsDendro = FALSE,
                       saveTOMs = TRUE,
                       saveTOMFileBase = "2-GSE50772_PBMC_TOM",
                       verbose = 5,
                       maxBlockSize = 15000)

save(net, file="2-net_output-original.RData")

##########################

Yet after the 3/3 TOM is created I see the following:

Error in fastcluster::hclust(as.dist(dissTom), method=“average” : NaN dissimilarity value.

Any thoughts on this? I have the three TOMs, but recutBlockwiseTrees() requires more than those to generate new modules. I'm guessing complete method instead of average would be better? What new arguments can I pass to overcome this? At this point I'm a bit desperate. Would it help to turn off PAM stage and go back to dynamic from hybrid?

Thanks,

Robert

I will have to add some more checks into the TOM calculation code. It seems that some probes were giving an NA or NaN in the correlation calculation, which then propagated into the TOM. Such probes are usually automatically flagged and filtered out by blockwiseModules, but the filtering will fail to catch some "pathological" special cases.

Do you have any missing values (NAs) in your data?