Comments on sequence normalization of tiling array expression.

Abstract

Methods to improve tiling array expression signals are needed to accurately detect genome features. Royce et al. provide statistical normalizations of tile signal based on probe sequence content that promises improved accuracy, and should be independently verified. Assessment of the sequence content normalization methods identified a problem: confounding of probe sequence content with gene structure (intron/exon) sequence content. Normalization obscured tile signal changes at gene structure boundaries. This and other evidence suggests that simple sequence normalization does not improve detection of genes from tile expression data.