Journal Article

Comments on sequence normalization of tiling array expression

Don Gilbert and Andreas Rechtsteiner

in Bioinformatics

Volume 25, issue 17, pages 2171-2173
Published in print September 2009 | ISSN: 1367-4803
Published online July 2009 | e-ISSN: 1460-2059 | DOI: http://dx.doi.org/10.1093/bioinformatics/btp389
Comments on sequence normalization of tiling array expression

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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.

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

Contact: gilbertd@indiana.edu

Journal Article.  1442 words.  Illustrated.

Subjects: Bioinformatics and Computational Biology

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