Trouble with gene dendrogram
0
0
Entering edit mode
jms2520 ▴ 10
@3184ac53
Last seen 19 months ago
United States

I am trying to plot my gene dendrogram while following the online tutorials for WGCNA. When using the function "table(bwnet$colors)" it shows that there should be 24 modules for my data. When I continue running the code for plotting the dendrogram (code below) I somehow keep getting a plot that looks like this. It seems to me that this is not consistent with there being 24 modules.

bwnet = blockwiseModules(datExpr0, maxBlockSize = 2000,
                     power = 6, TOMType = "unsigned", minModuleSize = 30,
                     reassignThreshold = 0, mergeCutHeight = 0.25,
                     numericLabels = TRUE,
                     saveTOMs = TRUE,
                     saveTOMFileBase = "TOM-blockwise",
                     verbose = 3)


# open a graphics window
sizeGrWindow(12, 9)
# Convert labels to colors for plotting
mergedColors = labels2colors(bwnet$colors)
# Plot the dendrogram and the module colors underneath
plotDendroAndColors(bwnet$dendrograms[[1]], mergedColors[bwnet$blockGenes[[1]]],
                    "Module colors",
                    dendroLabels = FALSE, hang = 0.03,
                    addGuide = TRUE, guideHang = 0.05)

table(bwnet$colors)



![> 0    1    2    3    4    5    6    7    8    9   10   11   12   13   14   15   16   17   18   19   20   21   22 
1287 4001 3115 2498 1774 1706 1135  735  484  305  299  269  265  157  117  111  104  101   77   71   68   63   61 
  23   24 
  60   44][1] 

enter image description here

Network RNASeq WGCNA • 1.2k views
ADD COMMENT
0
Entering edit mode

Hello,

I think we have the same problem, have you figured it out?

ADD REPLY

Login before adding your answer.

Traffic: 591 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6