Help selecting WGCNA soft thresholding power
0
0
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

enter image description here

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%

POWER WGCNA SOFT • 328 views
ADD COMMENT

Login before adding your answer.

Traffic: 1339 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6