take out the patient overl;ap from Agilent and RNAseq
new script to deDup AGilent
realised that I need to do positive coexpression for FACS

realised that I need to do positive coexpression for FACS relevance.
Changes many things in the script
end of day
adding annotations to V2
annotations functions
wrote script to run ssGSEA within R
got ssGSEA to work. should I scale?
need to compare ssGSEA and GSVA
read in patient data
end of day
annotate the script
redo Heatmap in functions script
tried to use heatmap.2 but failed
removing the module colors
added the analysis of more markers
update knitr Doc
end of day commit
last commit before rejig to 3SD
coverted the cutoff for signatures to 3sd