PCA of Combined Doane et al. and Farmer et al. Cohorts. First versus second component from Principal Components Analysis (PCA) of the combined cohorts from Farmer et al. (asterisks) and Doane et al. (circles) showing separation of molecular apocrine (green) and non-molecular apocrine (blue) tumors when performed on (A) natural-log scaled data quantile-normalized using Affymetrix-provided chip definition file (CDF); p-value = 0.369, (B) same as (A) with added XPN normalization step; p-value < 0.0001, and (C) same as (B) but using the AffyProbeMiner-provided CDF; p-value < 0.0001.
Sanga et al. BMC Medical Genomics 2009 2:59 doi:10.1186/1755-8794-2-59