WGCNA and microarray gene expression

Question

[mzezza]

Hi,

I've got a gene expression matrix (with GeneID and samples) and I'd like to perform a network analysis with WGCNA R package. Could anyone give me directions on how to process the data and possibly on how to proceed?

Thanks

Answer 1

[Kevin Blighe]

There are many threads and tutorials on WGCNA on the World Wide Web. Many people are unaware of the fact that WGCNA is not a Bioconductor package - it is on CRAN (CRAN has less stringent rules for packages when compared to Bioconductor). CRAN and Bioconductor are both repositories for R packages.

Nevertheless, you may want to start here: https://horvath.genetics.ucla.edu/html/CoexpressionNetwork/Rpackages/WGCNA/Tutorials/

You should proceed through each step of the tutorial, line by line, and aim to understand what is happening [at each step]. Once you finish the tutorial, try the method on your own data. Come back if you encounter error messages, but only after you have made a reasonable attempt to solve the error(s) yourself.

Kevin