MOTIVATION: 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. RESULTS: 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.
MOTIVATION: 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. RESULTS: 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.
Authors: Krishna R Kalari; Melanie Casavant; Thomas B Bair; Henry L Keen; Josep M Comeron; Thomas L Casavant; Todd E Scheetz Journal: In Silico Biol Date: 2006
Authors: David S Johnson; Wei Li; D Benjamin Gordon; Arindam Bhattacharjee; Bo Curry; Jayati Ghosh; Leonardo Brizuela; Jason S Carroll; Myles Brown; Paul Flicek; Christoph M Koch; Ian Dunham; Mark Bieda; Xiaoqin Xu; Peggy J Farnham; Philipp Kapranov; David A Nix; Thomas R Gingeras; Xinmin Zhang; Heather Holster; Nan Jiang; Roland D Green; Jun S Song; Scott A McCuine; Elizabeth Anton; Loan Nguyen; Nathan D Trinklein; Zhen Ye; Keith Ching; David Hawkins; Bing Ren; Peter C Scacheri; Joel Rozowsky; Alexander Karpikov; Ghia Euskirchen; Sherman Weissman; Mark Gerstein; Michael Snyder; Annie Yang; Zarmik Moqtaderi; Heather Hirsch; Hennady P Shulha; Yutao Fu; Zhiping Weng; Kevin Struhl; Richard M Myers; Jason D Lieb; X Shirley Liu Journal: Genome Res Date: 2008-02-07 Impact factor: 9.043
Authors: J Robert Manak; Sujit Dike; Victor Sementchenko; Philipp Kapranov; Frederic Biemar; Jeff Long; Jill Cheng; Ian Bell; Srinka Ghosh; Antonio Piccolboni; Thomas R Gingeras Journal: Nat Genet Date: 2006-09-03 Impact factor: 38.330