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Hello. I have problem to choose soft power for WGCNA. please guide me!! I have 501 sample (cancer=481 , normal=39) that download from TCGA database. Then, normalization and filtration was carried out using TCGA package. With this data I started using WGCNA for co-expression network analysis. For selecting soft threshold I see my R^2.sq is lower than 0.8 . please help me to chose best power. Thank you.
data_tcga_501_ordered_t <- t(data_tcga_501_ordered)
gsg <- goodSamplesGenes(data_tcga_501_ordered_t)
power <- c(c(1:10) , seq(from = 12 , to = 20 , by = 2))
sft <- pickSoftThreshold(data_tcga_501_ordered_t , powerVector = power , verbose = 5)
Power SFT.R.sq slope truncated.R.sq mean.k. median.k. max.k.
1 1 0.9520 1.500 0.955 7150.0 7630.00 10300
2 2 0.0707 0.163 0.125 3840.0 4030.00 7220
3 3 0.1880 -0.392 0.324 2300.0 2270.00 5340
4 4 0.3680 -0.717 0.522 1470.0 1340.00 4100
5 5 0.4630 -0.929 0.630 992.0 818.00 3230
6 6 0.5300 -1.080 0.704 694.0 513.00 2600
7 7 0.5710 -1.210 0.752 500.0 329.00 2130
8 8 0.5930 -1.330 0.785 368.0 216.00 1780
9 9 0.6280 -1.390 0.821 277.0 145.00 1490
10 10 0.6530 -1.440 0.846 212.0 99.00 1260
11 12 0.7050 -1.500 0.892 129.0 48.50 922
12 14 0.7410 -1.530 0.920 81.9 24.90 688
13 16 0.7630 -1.570 0.936 53.8 13.30 525
14 18 0.7650 -1.640 0.946 36.4 7.34 411
15 20 0.7760 -1.680 0.956 25.1 4.15 326
Not a Bioconductor package. Ask at biostars.org and add plots and well-formatted code.
Maybe you could expand the parameter to 40 or 50. Although, without seeing the stf plot, it's hard to comment. you could try: power <- c(c(1:10) , seq(from = 12 , to = 50 , by = 2))
A possible guide is to choose the value where the curve begins to stabilize ( this can be seen in the plot that you are not showing here), SO, it is also important to check values from the stf table (the one you are showing in the figure)
*On youtube, some people show short videos explaining about WGCNA, you could post WGCNA on youtube for visual explanations.