I was following the tutorials of WGCNA with a new dataset and I am getting an error about sizeRestrictedClusterMerge were the replacement is not of the same length as the values to replace:

> net <- blockwiseModules(biggermatrix, power = 7,
+                        TOMType = "signed", 
+                        networkType = "unsigned",
+                        minModuleSize = 30, reassignThreshold = 0, 
+                        mergeCutHeight = 0.25, numericLabels = TRUE, 
+                        pamRespectsDendro = FALSE, saveTOMs = TRUE,
+                        saveTOMFileBase = "DNA_RNA_TOM", verbose = 3)
 Calculating module eigengenes block-wise from all genes
   Flagging genes and samples with too many missing values...
    ..step 1
 ....pre-clustering genes to determine blocks..
   Projective K-means:
   ..k-means clustering..
   ..merging smaller clusters...
Error in clustDist[ii, ] <- if (intNetworkType == 1) 1 - abs(cr1) else 1 -  : 
  number of items to replace is not a multiple of replacement length
> traceback()
3: sizeRestrictedClusterMerge(datExpr, clusters = membership, clusterSizes = clusterSizes, 
       centers = centers, maxSize = preferredSize, networkType = networkType, 
       verbose = verbose, indent = indent)
2: projectiveKMeans(datExpr, preferredSize = maxBlockSize, checkData = FALSE, 
       sizePenaltyPower = blockSizePenaltyPower, nCenters = nPreclusteringCenters, 
       verbose = verbose - 2, indent = indent + 1)
1: blockwiseModules(biggermatrix, power = 7, TOMType = "signed", 
       networkType = "unsigned", minModuleSize = 30, reassignThreshold = 0, 
       mergeCutHeight = 0.25, numericLabels = TRUE, pamRespectsDendro = FALSE, 
       saveTOMs = TRUE, saveTOMFileBase = "DNA_RNA_TOM", verbose = 3)
> packageVersion("WGCNA")
[1] ‘1.67’

Is there any way to avoid this? Thanks

I forgot to mention that you may be able to avoid this error by changing the argument maxBlockSize (which I do recommend adjusting to the largest value your machine can take). I will of course try to track it down and fix it though.

Please try this development version:

https://www.dropbox.com/s/fuu73li4ajjfr3z/WGCNA_1.67-90.tar.gz?dl=0

Let me know if the problem persists.

Thanks!

Could you share the problem data?

Regarding a repository, not yet, just send your patches and suggestions to me.

Peter