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Question: Module trait association in wgcna
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gravatar for guliasitu40
6 weeks ago by
guliasitu40 • 80
guliasitu40 • 80 wrote:

Hi all, I am using wgcna for coexpression analysis of time series data. I have 48 samples in total (16 time points with 3 replicates). I have identified different modules based on gene correlation across all samples. After this I want to associate these modules to trait of interest. I have categorized these 16 time points into 5 time zones so I want to see which are the different modules which are associated with these 5 time zones. My trait data is:

samples  timezone1   timezone2    timezone3    timezone4    timezone5
dark11      1             0         0                 0        0
dark11_1    1             0         0                 0        0
dark9       1             0         0                 0        0
dark7       0             1         0                 0        0
dark7_1     0             1         0                 0        0
dark5       0             0         1                 0        0
dark5_1     0             0         1                 0        0

and so on

I want to ask if I am doing it right? or is there any other way to associate the traits to modules in categorical data? After identifying the modules related to every time zone, I want to identify intramodular connectivity and hub genes.
R rna-seq alignment assembly • 107 views
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modified 6 weeks ago by Kevin Blighe ♦ 71k • written 6 weeks ago by guliasitu40 • 80
1
gravatar for Kevin Blighe
6 weeks ago by
Kevin Blighe ♦ 71k
Republic of Ireland
Kevin Blighe ♦ 71k wrote:

I think that you are doing it correctly. I would use a binary logistic regression model here, something like:

summary(glm(timezone1 ~ pink_module, data = mydata, family = binomial(link = 'logit')))

You can also just perform a numerical correlation:

cor(as.numeric(mydata$pink_module), mydata$timezone1)
cor.test(as.numeric(mydata$pink_module), mydata$timezone1)

Regarding hub genes, I believe the WGCNA package already includes a function (or functions) for this (these).
ADD COMMENT • link modified 6 weeks ago • written 6 weeks ago by Kevin Blighe ♦ 71k

Thanks for the reply Kevin! Is the pink_module in your command contain only the genes names or expression values of the genes? and does mydata corresponds to traitdata that I have shown the the table?

ADD REPLY • link written 6 weeks ago by guliasitu40 • 80

In my code, pink_module would contain the module values returned by WGCNA, with there being 1 value per sample.

Yes, mydata would be of the form that you have shown, but also including extra columns for the modules (pink, blue, green, etc)

ADD REPLY • link written 6 weeks ago by Kevin Blighe ♦ 71k

Lot of thanks Kevin, it worked perfectly fine. Sorry to bother you again, but I am getting negative scale independence (y-axis). I have also removed genes which were not suitable for the anlaysis. Does the negative scale dependence showing that my data don't follow the scale free topology or does it shows anything else? Or anything wrong with my data? I have considered softpower threshold = 12 according to WGCNA FAQ.

ADD REPLY • link modified 6 weeks ago • written 6 weeks ago by guliasitu40 • 80
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