Dear list,

I recently read a Bioconductor post where the developer of the WGCNA suggested the use of the package for RNA-seq data analysis after implementing a variance stabilization normalization to the raw counts. I have read the tutorials and run the example dataset at http://labs.genetics.ucla.edu/horvath/CoexpressionNetwork/Rpackages/WGCNA/Tutorials/index.html. I would like to apply WGCNA to my RNA-seq data consisting of 1000 transcripts whose expression is measured for 50 triplicated cell types (approximately 150 samples) and derive gene networks.

I would like to ask if WGCNA can be used successfully in this kind of heterogeneous dataset where, for most of the transcripts, the various cell types expression patterns might differ substantially (so that a variance stabilizing transformation will not give me approximately normal distribution for each transcript; it would rather be a mixture of normal distributions).


Thank you,
Pan  




 		 	   		  
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