Hi,
Im new to the WGCNA r package, and Im wanting to identify modules and eigengenes from my data set.
My data is genes as columns and samples as rows (I can manipulate this if needed).
Does anyone have sample code for something like this? None of the sample codes have been useful.
The official tutorials can be found on this Dropbox, shared by Peter Langfelder since the main website is unavailable.
It's not extremely straightforward, but if you pick either "Simulated" or "FemaleLiver" and go through the pdfs in order (e.g. Simulated-00, then Simulated-01, etc ...), everything is explained. You might have to check the help of individual functions (e.g. ?plotDendroAndColors) to really understand what a given step is doing.
Otherwise, there is also a tutorial here that mostly follows the same order, with fewer explanations but more modern syntax.
If you have more specific questions about individual steps, feel free to ask.