# 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)

• You will need to provide more detail. How big was the data from which you calculated the network (how many genes) and how did you determine geneTree? Jun 15, 2019 at 22:32
• I have 12711 genes after filtering and have added the additional code above. It has worked with the simple Automatic, one-step network construction and module detection and Step-by-step network construction and module detection but not when trying with 2 blocks. Thank you kindly Jun 16, 2019 at 7:23