What pipeline should I use with WGCNA?

Question

[madkitty]

We need to compare 3 datasets controls (containing information for about 7 cell lines) to one dataset containing 10 replicates. I was about to use WGCNA to obtain gene overlaps, p-value and module preservation between controls and the replicates. All of these data are from micro array data.

I've been reading the WGCNA tutorial and the Miller tutorial as well, all of these are very confusing, I don't see any step by step clear pipeline written in plain English anywhere I look. What pipeline would you suggest? Please point me out to the right direction!

Answer 1

[omicj]

WGCNA is the great application but it's bit hard to follow the steps in the tutorial document. I guess there is too much information as well as people might have different direction for their questions.

I guess the best tutorial (at least for me) was found in O'Dushlaine et al., 2015 http://www.nature.com/neuro/journal/v18/n2/abs/nn.3922.html

Please see the supplementary code, neatly written by Parikshak (+ nice example of scientific sharing). Also see this code as well: http://labs.genetics.ucla.edu/horvath/htdocs/CoexpressionNetwork/developingcortex/

If you are familiar with R, you will easily follow the step for getting your answers. If not, the code will help you understand the structure of data for downstream analysis.

Cheers

[Smriti]

the link that u have suggested seems to be corrupted please could u reshare