WGCNA soft threshold power showing very strange values
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aleeeceeea • 0
@aleeeceeea-19784
Last seen 3.5 years ago
London

My plot of soft threshold (power) vs. scale free topology model fit looks very different from the tutorial plot & other WGCNA plots online.

It starts with a power of 1 with a value of over 0.8, then rapidly decreases to values around 0.2 for powers over 3.

Does this mean I should use a softPower of 1?

The data is normalised bacterial OTUs relative abundance levels (from 16s rRNA profiling).

enter image description here

image of my plot: https://ibb.co/Lgg4szy

wgcna soft threshold r scale independence scale free topology model fit • 1.5k views
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@peter-langfelder-4469
Last seen 1 day ago
United States

I recommend reading the relevant part of WGCNA FAQ, especially question 6. I don't have any experience with metagenomic data, so I can't give you a more informed answer, but it is always helpful to plot the sample clustering tree and/or PCA plot to make sure nothing weird is going on.

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