Uploaded to collaboration site by	Alfred Hero	Apr 30, 2008 
File                           Description
Adjusted_rho.rma.226.affy.csv   -- A-CDF data adjusted for batch effects using EB
Adjusted_rho.rma.226.ccdf.csv	  -- C-CDF data adjusted for batch effects using EB
rho.rma.226.affy.csv            -- normalized data using Affymetrix CDF
rho.rma.226.ccdf.csv            -- normalized data using Custom CDF
sample.id.maching.csv           -- Table mapping CEL files to samples
                                   subject but not time point
eaid2subject-timepoint-all.txt  -- mapping from eaid to subject,timepoint
                                   for the combined data sets
                                   eaids for batch 1 begin with 3
                                   eaids for batch 2 begin with 5
                                   
The Adjusted... are normalized taking into account batch effects.
There are two batches.  The adjustment is done according to 

W. Johnson, C. Li, and A. Rabinovic, “Adjusting batch effects in microarray
expression data using empirical bayes methods,” Biostatistics, vol. 8, no. 1, 
pp. 118–127, 2007.

The .affy.csv normalization is done using RMA - Robust Multichip Average method
developed according to

Rafael. A. Irizarry, Benjamin M. Bolstad, Francois Collin, Leslie M. Cope,
Bridget Hobbs and Terence P. Speed (2003), Summaries of Affymetrix GeneChip
probe level data Nucleic Acids Research 31(4):e15

The .ccdf.csv normalization was done using the custom chip definition file
compiled by Michigan. You can find more information in

Evolving Gene/Transcript Definitions Significantly Alter the Interpretation
of GeneChip Data. Nucleic Acid Research 33 (20), e175.

Basically, it provides a more precise probe mapping file than the default
Affymetrix one.  It produces one measurement per gene. 
   
Caveat -- in eaid2subject-timepoint-all.txt for batch 2 there are
 2 eaids for each subject-timepoint, but only one them has data
 in the summary or normalized data files (fortunately it seem to
 be the same one.)   I will have the database table redone to
 clean this up.  But the current mapping can be used.