First .Rmd seems to be working. All functions are working.
.gitignore updated to ignore .Rmd output files (e.g. .html)
added calcIndicator.R
continuing to edit first .Rmd file
Added removeBioReps.R to /functions and used it in AllegroSetup.R to remove the biological replicates from exprData before data filtering.

Without removing the bioReps, many COPD*Cancer genes come up as significant... perhaps decreasing the number of genes tested will help with this as well.
Finished for the day 2014-06-05. Ran model using COPD_R7
see .html file from today for thoughts for next time