Different result from WGCNA tutorial I

Question

[afli]

Dear friends,

I am running the WGCNA tutorial code. In tutorial I, section2.c, my results are different from the tutorial(https://horvath.genetics.ucla.edu/html/CoexpressionNetwork/Rpackages/WGCNA/Tutorials/FemaleLiver-03-relateModsToExt.pdf).

In detail, in the 2.c.2 of the 'FemaleLiver-03-relateModsToExt.pdf',

>table(bwLabels) #The whole code is in the tutorial I of WGCNA(https://horvath.genetics.ucla.edu/html/CoexpressionNetwork/Rpackages/WGCNA/Tutorials/), you would spend 10 mins to perform the step1, step2.a, step2.b, and this line is in step2.c.

My result is

bwLabels
0   1   2   3   4   5   6   7   8   9  10  11  12  13  14  15  16  17  18  21 
147 568 462 531 225 275 125 207  51 120 100 100 146  83  77  76  44  42  34  98 
22 
89

The tutorial is

bwLabels
0   1   2   3   4   5   6   7   8   9  10  11  12  13  14  15  16  17  18  19
142 472 470 479 271 327 130 209 153 121 100 100 104  77  73  81  40  42  34  91
20
84

So they are different, I wonder why the same code and same data would produce the different results. The data are in the same site of the tutorial, you can easily get them and spend a few minutes to run the tutorial. Could anyone please test the tutorial and give me some advice? Thank you very much!

Aifu.

Answer 1

[Kevin Blighe]

My result:

table(bwLabels)
bwLabels
  0   1   2   3   4   5   6   7   8   9  10  11  12  13  14  15  16  17  18  21 
147 568 462 531 225 275 125 207  51 120 100 100 146  83  77  76  44  42  34  98 
 22 
 89

I put it down to one or more of the following:

1. an old tutorial whose content has not been updated for a long time (2014)
2. a modern R environment where the base functions have been modified since WGCNA was initially developed
3. the WGCNA functions themselves have been modified but the tutorial never updated.

Kevin

[afli]

All right! Thank you Kevin!

[afli]

Hi Kevin, you're right. I use R3.1.2, and WGCNA1.41.1, the result is the same with the tutorial.

[Kevin Blighe]

Cool!