Dear all,

I'm learning WGCNA via following its tutorial and example (Network analysis of liver expression data in female mice). However, I came across some questions, happy to know your comments.

Regarding visualizing the gene network, the tutorial says:

# Calculate topological overlap anew: this could be done more efficiently by saving the TOM
# calculated during module detection, but let us do it again here.
dissTOM = 1-TOMsimilarityFromExpr(datExpr, 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 nicer plot
diag(plotTOM) = NA;
# Call the plot function
TOMplot(plotTOM, geneTree, moduleColors, main = "Network heatmap plot, all genes")

Here, my question is while the power was determined 6 (power=6) in the previous line, why the power of 7 was used in dissTOM^7?

Also, my obtained heatmap had a red background. I solved this issue using this post.

however, as you may see in the above image, the plot colors are not identical to the corresponding plot in the tutorial. I would like to know if it is the matter, I mean does it impact the results?


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