PLEASE NOTE:

The original labels of the .CEL file names in the Novartis data contain
errors in the SM male diets. THEREFORE, the columns of the RMA data file
"Affy061406.rma.dat" CONTAIN THESE ERRORS! 

The mistake is that in the SM males, the two diet conditions were transposed..
SO:  the 3 SM males listed as high fat (SM-M-HF-1,2,&3) are actually the 6% Chow males
AND: the 3 SM males listed as 6% chow (SM-M-6C-1,2,&3) are actually the High Fat males

The CORRECTED design file is - "Novartis_12strains_Paigen_design_file_083106_corrected.dat"
The original, UNCORRECTED design file is - "Affy.061406.Final.design.rma.dat"

ALSO:

"Gene Expression" = Affy061406.rma.dat - the RMA processed signal intensities
"Experimental design file" = Novartis_12strains_Paigen_design_file_corrected_030807.dat

The design file columns:
Array - name of the CEL file
Dye - dye color (always =1 for one color Affy arrays here)
Sex - sex of the mouse
Strain - strain of the mouse
Diet - Diet fed. 6C = 6% chow (low fat); HF = high fat 
Sex_Diet - the Sex/Diet combination of the mouse
Group - teh Sex/Diet/Strian combination of the mouse
Sample - the sample from which the RNA was derived (always biologically unique RNA on each array)
BIOL_REP - biological replicate from a grouping