Added sessionInfo() to the AllegroSetup.R script so that when using RMarkdown to output html files the html includes R session info
edited calcIndicator to [hopefully] return indicator with only levels 1-4 and not including a level 0
Created generate_heatmap.R and return_cluster.R to work with expressionSet objects. Updated removeFactorLevel because there was extra code.

2014-06-09 analysis for squamous vs moderate-severe COPD
Edited AllegroSetup.R to use full pathname of sourceDir.R and loadFunctions.R instead of relative to the working directory
Edited loadFunctions.R to use full pathname of /functions directory, i.e. /protected/projects/pulmarray/Allegro/COPD_Cancer/functions instead of ../../functions
altering the .gitignore file to include files\n related to RMarkdown
Starting to use RMarkdown and Limma