These R scripts will generate all the expression summary datasets and 
then re-create figure 7 from the Genome Biology article.

The expression summary datasets that were created outside of R are not included here. 


PACKAGES USED:
affy (www.bioconductor.org): 1.4.31
goldenspike (www.elwood9.net/spike):  0.3


ORDER OF COMMANDS:

cd data.affybatch
R CMD BATCH data.orig.R

cd ../scripts.make.exprs
R CMD BATCH commands.constant.R
R CMD BATCH commands.loesssubset.R
R CMD BATCH commands.quantile.R
R CMD BATCH commands.quantile2.R
R CMD BATCH commands.invar2.R
R CMD BATCH commands.medpolish.R
R CMD BATCH commands.loess2.R

cd ../scripts.do.comps
R CMD BATCH command.pierre.R
R CMD BATCH command.make.ro.R
R CMD BATCH command-fig7.R
