readdata.R	           
====================
read the GPR files    

Input: SampleData(Kidney2).txt: Holgers table with patient and experiment annotation
       175 Arrayvision files in directory Echip
       Table1-General.RData: an extended table with patient annotations	

Output: pat.rda
        hybanno.rda
	qua.rda

qc.R
=================
calculate and plot QC statistics

Input:  ny175.rda
Output: $BGMETHOD/cv.rda


runvsn74.R (see also runvsn.R)
=================
run the normalization with vsn
use only the "good" hybs selected by Holger

Input:    qua.rda
	  selected_chiphybs.txt	
Output:   ny74.bgfilt.rda  (smoothed local background was used)


makecloneanno.R
======================================
output: cloneanno.rda
        spotanno.rda

makeeset.R
==========
1. average over duplicate spots
2. build expression set

Input: ny74.bgfilt.rda
       spotanno.rda
       pat.rda
Output:
      eset74.rda
Requires:
      Biobase


test.R
==========
perform statistical tests for each gene,
estimate FDR
Results go into the directory Results2/
(newest version, after updating sample annotations 
in 11-03)

Output:
	Results2/cctest.results.rda
	Results2/subtype.results.rda
	Results2/cox.results.RData
	Results2/test.FDR.results*.RData

	Genelists generated by the function write.clonelist:
	
	Results2/*.html
	Results2/*_resultat.txt