I am working with Hovarth's tutorial (https://horvath.genetics.ucla.edu/html/CoexpressionNetwork/Rpackages/WGCNA/Tutorials/index.html) to explore connections between gene expression and formed modules using a network analysis approach (R package WGCNA) in my RNAseq data set.
While exploring step 5 of Part 1 (Network visualization using WGCNA functions; See R script here: https://horvath.genetics.ucla.edu/html/CoexpressionNetwork/Rpackages/WGCNA/Tutorials/FemaleLiver-05-Visualization.R) I receive an error that I cannot seem to figure out. See below for code:
# Calculate topological overlap dissTOM = 1-TOMsimilarityFromExpr(datExprSe, power = 6); # Transform dissTOM with a power to make moderately strong connections more visible in the heatmap plotTOM = dissTOM^7; # Set diagonal to NA for a cleaner, more readable plot diag(plotTOM) = NA; # Call the plot function sizeGrWindow(9,9) # left as Hovarth default TOMplot(plotTOM, geneTree, moduleColors, main = "Network heatmap plot, all genes") # After running this I get the error seen below in bold
Error in x[, iy] : subscript out of bounds
Note: I ran the entire tutorial without issue using Hovarth's data set and code. My input is modeled after how their tutorial was created. Any help/advice is welcome!