Gene filtering. A total of 22 283 probe sets were filtered using a noise envelope to eliminate genes with little cross-chip variability. The noise envelope was estimated on 14 HeLa cell lines and 5 Strategene samples. Two filters were used, resulting in gene sets of 6997 (α = 0.999) and 4204 (α = 0.9999) probe sets. Unsupervised analyses were done using the 4204-gene filter. Supervised analyses were done using the 6997-gene filter.