Dear connections
I am testing several datasets using the wgcna tool. I am a bit confused with the meaning of two columns of the output table calculated for the soft threshold power function: "SFT.R.sq" vs "truncated.R.sq" columns.
Please, let me please explain myself with two examples:
Let's to suppose that I choose up the SFT power of 25 in the ntw1 (left plot - red-square) as show in the output table, the "SFT.R.sq" column sets this power with a value of 6.96911e-01, its convertion would be 0.1434, meaning that this value wouldn't adjust well to a free topology scale (TOM), but then the next column called "truncated.R.sq" has value of 0.6942. In fact an abline in 0.70 in the plot match the truncated.R.sq" as you can see. Thus, Why the too far distance between the two metrics?
Now let's to see the next table on the right, focus on the SFT power of 28 (blue-square), the "SFT.R.sq" is ~0.74, but again the "truncated.R.sq" is ~0.913. Less distant but still with a moderate difference, Why?
Please, somebody can explain to me, what is the more accurrate column's reference in this table to choose a SFT? and to provide a brief explanation of why?
Thanks by advance
Cynthia
I think the SFT in Ntw1 represents a scientific notation, making it 0.6969 rather than 0.1434. This value is indeed much closer to the truncated R.sq value of 0.6942.
As for the difference between SFT and truncated, I am interested as well as I currently do not know the difference.
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