Question

WGCNA Choosing soft threshold power below R^2 0.8

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emilymily77 • 0

@e7919d9f

Last seen 8 weeks ago

South Korea

Hi, I'm having problem with picking soft threshold power in WGCNA. They all have SFT. R. sq lower than 0.8, so I have trouble with picking soft threshold power. What power should I pick?

   Power SFT.R.sq   slope truncated.R.sq mean.k. median.k. max.k.
1      1  0.73200  2.3400          0.896   704.0    734.00  995.0
2      2  0.30700  0.5700          0.641   407.0    424.00  700.0
3      3  0.00023  0.0131          0.383   265.0    271.00  522.0
4      4  0.08980 -0.2580          0.504   185.0    186.00  408.0
5      5  0.22200 -0.4520          0.619   135.0    133.00  328.0
6      6  0.32800 -0.6270          0.685   103.0     99.50  269.0
7      7  0.41800 -0.7310          0.759    80.5     76.00  225.0
8      8  0.48800 -0.7980          0.823    64.4     59.70  191.0
9      9  0.53600 -0.8660          0.847    52.4     47.60  164.0
10    10  0.57100 -0.9300          0.869    43.4     38.90  142.0
11    12  0.62500 -0.9900          0.913    30.8     26.80  110.0
12    14  0.67400 -1.0300          0.940    22.8     18.90   87.1
13    16  0.71800 -1.0700          0.954    17.4     13.70   70.4
14    18  0.75200 -1.0900          0.956    13.7     10.10   57.9
15    20  0.77800 -1.1400          0.973    10.9      7.73   49.1

Here is the figure

WGCNA • 260 views

ADD COMMENT • link updated 10 weeks ago by Lluís Revilla Sancho ▴ 760 • written 10 weeks ago by emilymily77 • 0

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This is not a bioconductor pacakge, but have you considered that something might be off with your data? Do you have enough samples of each category? Where all normalized the same way?

ADD REPLY • link 10 weeks ago Lluís Revilla Sancho ▴ 760