I'm running WGCNA to find consensus modules between two experiments.
I'm stuck at 'plotDendroAndColor' step due to the mismatch of the number of 'consTree' and 'moduleColors' as shown below. As a result, the plot showed only the dendrogram but no colored modules.
> length(moduleColors)  17459 >consTree Call: fastcluster::hclust(d = consTomDS, method = "average") Cluster method : average Number of objects: 17398
I set the maxBlockSize=30000 to contain all the object in a single cluster, but still some of the objects seemed to be gone after running 'blockwiseConsensusModules'.
> net = blockwiseConsensusModules( multiExpr, power = 6, minModuleSize = 30, deepSplit = 2, pamRespectsDendro = FALSE, maxBlockSize=30000, mergeCutHeight = 0.25, numericLabels = TRUE, minKMEtoStay = 0, saveTOMs = TRUE, verbose = 5) > consMEs = net$multiMEs; > moduleLabels = net$colors; > moduleColors = labels2colors(moduleLabels) > consTree = net$dendrograms[]; > plotDendroAndColors(consTree, moduleColors, "Module colors", dendroLabels = FALSE, hang = 0.03, addGuide = TRUE, guideHang = 0.05, main = "Consensus gene dendrogram and module colors")
Can anyone help me to solve this?