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Bioinformatics Advance Access first published online on July 4, 2009
This version published online on July 6, 2009
Bioinformatics, doi:10.1093/bioinformatics/btp389
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© The Author (2009). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

Comments on sequence normalization of tiling array expression

Don Gilbert 1,* and Andreas Rechtsteiner 2,3

1Department of Biology, Indiana University, Bloomington, IN, USA
2Center for Genomics & Bioinformatics, Indiana University, Bloomington, IN, USA
3Department of Biology, University of California Santa Cruz, Santa Cruz, CA, USA

*To whom correspondence should be addressed. Prof. Donald Gilbert, E-mail: gilbertd{at}indiana.edu


  Abstract

Motivation: Methods to improve tiling array expression signals are needed to accurately detect genome features. Royce et al (2007) 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.

Availability: http://wfleabase.org/genome-summaries/tile-expression/tileseqnorms/

Contact: gilbertd{at}indiana.edu

Associate Editor: Dr. Trey Ideker

Received on April 2, 2009; revised on June 18, 2009; accepted on June 19, 2009

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