read me.txt

Check out the three csv files: these are necessary to run the eigengene-trait relationship tests (normalized gene counts, metadata, and each module-gene assignment)
You can give files the same exact names for ease but any file names including the strings "count" "meta" and "module" will be recognized.

Note for metadata: you can have as many columns (i.e., traits) as you want and binary character variables (e.g., yes or no) are fine 
as they'll be converted to numerical values automatically


Instructions for running:

First run Eigengenes.R to make sure packages are installed and to establish the Eigengenie function.

If it gives no errors, then open Run_eigengenie.R, set the dir argument to your with your three necessary CSVs,
then run.