Entering edit mode
9 days ago
TNF_alpha
•
0
sft <- pickSoftThreshold(LOG_TPM_COUNT,
+ powerVector = power,
+ networkType = "signed",
+ verbose = 5)
pickSoftThreshold: will use block size 1192.
pickSoftThreshold: calculating connectivity for given powers...
..working on genes 1 through 1192 of 1192
Power SFT.R.sq slope truncated.R.sq mean.k. median.k. max.k.
1 1 0.420 146.000 0.388 1130.0 1130.0 1140
2 2 0.407 72.200 0.381 1060.0 1070.0 1090
3 3 0.490 36.100 0.374 1010.0 1010.0 1050
4 4 0.491 27.000 0.374 952.0 958.0 1000
5 5 0.495 21.800 0.378 901.0 908.0 960
6 6 0.489 18.100 0.372 852.0 860.0 920
7 7 0.482 15.400 0.366 807.0 815.0 882
8 8 0.367 15.400 0.328 764.0 773.0 845
9 9 0.354 13.500 0.320 723.0 732.0 810
10 10 0.446 10.600 0.355 685.0 694.0 776
11 12 0.737 5.040 0.882 614.0 625.0 714
12 14 0.743 4.320 0.869 552.0 562.0 656
13 16 0.264 5.290 0.254 496.0 506.0 604
14 18 0.658 3.060 0.769 446.0 455.0 556
15 20 0.715 2.710 0.789 401.0 410.0 512
16 22 0.728 2.450 0.775 361.0 369.0 471
17 24 0.760 2.490 0.751 325.0 333.0 434
18 26 0.635 2.340 0.609 293.0 300.0 400
19 28 0.659 2.240 0.606 264.0 270.0 369
20 30 0.669 2.020 0.596 238.0 244.0 341
21 32 0.668 1.850 0.581 215.0 220.0 314
22 34 0.662 1.700 0.568 194.0 199.0 290
23 36 0.651 1.580 0.551 176.0 180.0 268
24 38 0.619 1.380 0.510 159.0 162.0 247
25 40 0.605 1.260 0.502 144.0 147.0 229
26 42 0.607 1.140 0.526 130.0 133.0 211
27 44 0.598 1.050 0.539 118.0 120.0 195
28 46 0.576 0.954 0.551 107.0 109.0 181
29 48 0.561 0.876 0.578 96.8 98.5 167
30 50 0.498 0.795 0.568 87.7 89.1 155
None of the point in my Scale free topology model fit, signed R^2 crossed 0.8 and they are irregularly distributed. How to select the soft power in this case?
sft <- pickSoftThreshold(count_mat.subset,
powerVector = power,
networkType = "signed",
verbose = 5)
a1 <- ggplot(sft.data, aes(Power, SFT.R.sq, label = Power)) +
geom_point() +
geom_text(nudge_y = 0.1) +
geom_hline(yintercept = 0.8, color = 'red') +
labs(x = 'Power', y = 'Scale free topology model fit, signed R^2') +
theme_classic()
a2 <- ggplot(sft.data, aes(Power, mean.k., label = Power)) +
geom_point() +
geom_text(nudge_y = 0.1) +
labs(x = 'Power', y = 'Mean Connectivity') +
theme_classic()
soft_power <- 6
temp_cor <- cor
cor <- WGCNA::cor
bwnet <- blockwiseModules(count_mat.subset,
maxBlockSize = 30000, # As I have 56948 genes
TOMType = "signed",
power = soft_power,
mergeCutHeight = 0.25,
numericLabels = FALSE,
randomSeed = 1234,
verbose = 3)
cor <- temp_cor
module_eigengenes <- bwnet$MEs
> table(bwnet$colors)
#result:
turquoise
1192 # got "pickSoftThreshold: will use block size 1192." while using pickSoftThreshold
I tried with soft_power 12 and soft_power 6. Each time I got only one module. What am I doing wrong here?!!! My pc1 = 9% pc2 = 6%