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 sizeGrWindow(9,9) 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?