Question: WGCNA blockwiseConsensusModules : number of colors and objects in dendrogram don't match
gravatar for mbk0asis
10 months ago by
Korea, Republic Of
mbk0asis570 wrote:


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)
[1] 17459


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[[1]];

 > 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?

Thank you!

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