# NOTES for: 'Gene Expression in Mouse Chromosome Substitution Strains' in Mammalian Genome
# Shockley, Keith R. and Churchill, Gary A. (2006)
#
# Calculations were performed in R/maanova version 0.98-7
#
# The RMA expression measures generated in the "original_liver_samples" include the 92 arrays 
# examined in the published study plus 8 additional arrays. The 8 additional arrays 
# correspond to 2x replication for both sexes in two different F1 crosses - B6 x AJ and 
# AJ x B6. 
#
# There are 3 different data files for the liver experiment:
# (1) "data.norm_original_liver_samples.dat" <- only normalized original 92 + 8 arrays together
# (2) "data.norm_repeated_liver_samples.dat" <- only normalized repeated 12 arrays together
# (3) "data.norm_all_liver_samples.dat"      <- normalized original + repeated arrays together
#
# In the liver experiments, 185 out of 45,101 probe sets were determined to be outliers and 
# were subsequently removed from the analysis. These 185 probe sets "liver_outliers.Rdata" 
# object. No such outliers were found in the kidney study.
#
# The file "affy.CHR.bp.positions.090605.csv" was prepared by parsing the Affymetrix
# annotation file. Probe sets that did not uniquely map to a chromosomal location were
# removed and associated information for that probe set was designated as "0"
#
# Key calculations are provided in the R scripts given here. Instances in which calculations
# were performed in the kidney study can be derived from the scripts detailing the analyses in
# the liver
#
# Affymetrix annotations are updated regularly (see www.Affymetrix.com). We used annotations 
# from 2004 in this analysis
#
# Two different chromosome enrichment analyses were performed in each tissue: 
# (1) cis-QTL
# (2) trans-QTL
# No significant enrichment was found for trans-QTL, as noted in the paper
#
# Celera SNP data was derived from 'SNPview' and extracted into 1 .CSV file per chromosome
# which are labeled, e.g., "CHR_1.csv", "CHR_2.csv", etc.
#
# The file "gene_sets_master_backup.csv" contains manually collected sets of genes from
# Biocarta and GO terms that were mapped using NetAffx
#