Error Code in WGCNA: Dealing with large data sets: block-wise network construction andmodule detection I am comparing single block module detection with 2 block module detection in WGCNA.

Does anyone know what this relates to? I have rechecked and rechecked my codes for both the single and 2 module detection and cannot see an error. Thank you

I get the error code: 

Error in plotOrderedColors(dendro$order, colors = colors, rowLabels = rowLabels,  : 
  ERROR: length of colors vector not compatible with number of objects in 'order'.


Using the following code:

net= blockwiseModules(Th1_h5, power=6,
                      TOMType = "signed", minModuleSize=30,
                      reassignThreshold =0, mergeCutHeight = 0.25,
                      numericLabels = TRUE, pamRespectsDendro = FALSE,
                      saveTOMs = TRUE,
                      saveTOMFileBase = "PBCreponseTOMB",
                      verbose= 3 
mergedColors = labels2colors(net$colors)

plotDendroAndColors(net$dendrograms[[1]], mergedColors[net$blockGenes[[1]]],
                    "Module colors",
                    dendroLabels = FALSE, hang = 0.03,
                    addGuide = TRUE, guideHang = 0.05)
moduleLabels = net$colors
moduleColors = labels2colors(net$colors)
MEs = net$MEs
geneTree = net$dendrograms[[1]]

bwet = blockwiseModules(Th1_h5, maxBlockSize = 8000,
                        power=6, TOMType = "signed", minModuleSize = 30,
                        reassignThreshold = 0, mergeCutHeight = 0.25,
                        numericLabels = TRUE,
                        saveTOMs = TRUE, 
                        saveTOMFileBase = "Th1_NR_R_TOM-blockwise",
                        verbose=3)
bwLabels = matchLabels(bwet$colors,moduleLabels)

bwModuleColors = labels2colors(bwLabels)


plotDendroAndColors(geneTree,
                    cbind(moduleColors, bwModuleColors),
                    c("Single block", "2 blocks"),
                    main = "Single block gene dendrogram and module colours",
                    dendroLabels = FALSE, hang = 0.03,
                    addGuide = TRUE, guideHang =  0.05)
The problem is that blockwiseModules split your data into (probably 3) blocks, because the default maxBlockSize is 5000 and smaller than the number of genes in your data. If you have enough RAM (16GB is recommended for 12k genes, but 8GB just might be enough), rerun blockswiseModules again with maxBlockSize raised to above the number of your genes. Since you were able to run the function with maxBlockSize=8000, hoepfully you'll be able to do the single block calculation.