some wgcna issues
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@zhouxiuqing-7455
Last seen 9.1 years ago

Hi,

We are using WGCNA to analyze some gene expressions. We have 40 tumor-normal paired samples and there are batch effects. So we first use COMBAT to remove batch effects on log(rpkm+1) scaled expression data . And then use the log(T/N) as the input of WGCNA.  Is the data we use OK  or we should use the original data without batch  removed or we should use only the tumor expression to WGCNA? 

   For some of our trait data, only 0 and 1 are provided. Can these trait data be used to do the "Module−trait relationships" analysis?

   In addition, we found that the number of genes differs much in different modules as follows:

     2272 genes_in_black.txt 
     3862 genes_in_blue.txt 
     74 genes_in_cyan.txt 
     38 genes_in_darkred.txt 
     2059 genes_in_green.txt 
     64 genes_in_grey60.txt 
     67 genes_in_lightcyan.txt 
     61 genes_in_lightgreen.txt 
     52 genes_in_lightyellow.txt 
     1156 genes_in_magenta.txt 
     73 genes_in_midnightblue.txt 
    393 genes_in_purple.txt 
     52 genes_in_royalblue.txt 
     140 genes_in_tan.txt 
     3930 genes_in_turquoise.txt 
     14293 total 

    Is the result normal? Does anyone know?

Best regards!

wgcna • 2.4k views
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@peter-langfelder-4469
Last seen 1 day ago
United States

I suggest removing batch effects and then using all 40 samples as input to WGCNA. Then you can look for modules that are over/under-expressed in tumor samples vs. normal, or associated with other variables you have.

You could use the T/N or just T expression indices if you have interesting sample traits that are defined only in the tumor samples; otherwise I don't see a point in leaving the normal samples out or doing T/N.

You can use a binary trait as you would use a continuous trait, simply correlate it with eigengenes. You could also use a Student t-test to measure the association of binary traits with eigengenes.

And yes, numbers of genes in modules do tend to vary widely, from a few thousand down to the minimum specified module size, which is usually 20 or 30.

Peter

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@zhouxiuqing-7455
Last seen 9.1 years ago

Hi Peter,

    You mean that we should use 40 pairs(i.e. 80) samples as input to WGCNA?

Thank you !

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@peter-langfelder-4469
Last seen 1 day ago
United States

Yes, the more samples the better. I should have said though that the most appropriate way of running WGCNA depends on what sample information you have and what are the questions you want to answer.

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@zhouxiuqing-7455
Last seen 9.1 years ago

Thank you very much Peter, I will try.

Best regards!

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