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!