Trouble generating a dendrogram with colored gene modules using WGCNA for large RNA-seq experiment

Question

[aehall26]

Hi all,

I am running WGCNA on my big gene expression data set, and running into a bunch of errors. I appreciate any help in advance that you can provide in navigating these!

First, the graph generated to choose the power is wacky looking.

I chose 28, as I figured this was above the threshold. But is that elbow cause for concern?

Second, going forward with a power of 28, although I have also tried other powers and gotten the same error: "Length of colors vector not compatible with number of objects in 'order'."

When I run the length of colors and order are different. Are they supposed to be the same?

 length(bwnet28$colors)
[1] 39

length(bwnet28$dendrograms[[1]]$order)
[1] 29559

I've also gotten strange errors saying for example:

Error in rect(trafo1$x, trafo1$y, trafo2$x, trafo2$y, col = as.character(C[,  : 
  invalid color name 'salmon.1'

For reference, here is the plotting code for the creation of the dendrogram:

bwnet28 <- blockwiseModules(norm.counts,
                          maxBlockSize = 30000,
                          minModuleSize = 30, 
                          reassignThreshold=0,
                          TOMType = "signed",
                          power = soft_power,
                          mergeCutHeight = 0.25,
                          numericLabels = F,
                          randomSeed = 1234,
                          verbose = 3)
cor <- temp_cor

#module eigen genes 
module_eigengenes <- bwnet28$MEs
head(module_eigengenes)
table(bwnet28$colors)
plotDendroAndColors(bwnet28$dendrograms[[1]], cbind(bwnet28$unmergedColors, bwnet28$colors),
                    c("unmerged", "merged"),
                    dendroLabels = FALSE,
                    addGuide = TRUE,
                    hang= 0.03,
                    guideHang = 0.05)

Any help here is much appreciated, as is evident, I am new to this!