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Bioinformatics Advance Access originally published online on July 9, 2009
Bioinformatics 2009 25(18):2369-2375; doi:10.1093/bioinformatics/btp425
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© 2009 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

TileProbe: modeling tiling array probe effects using publicly available data

Jennifer Toolan Judy 1 and Hongkai Ji 2,*

1Department of Mental Health and 2Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, 615 North Wolfe Street, Baltimore, MD 21205, USA

*To whom correspondence should be addressed.


  Abstract

Motivation: Individual probes on an Affymetrix tiling array usually behave differently. Modeling and removing these probe effects are critical for detecting signals from the array data. Current data processing techniques either require control samples or use probe sequences to model probe-specific variability, such as with MAT. Although the MAT approach can be applied without control samples, residual probe effects continue to distort the true biological signals.

Results: We propose TileProbe, a new technique that builds upon the MAT algorithm by incorporating publicly available data sets to remove tiling array probe effects. By using a large number of these readily available arrays, TileProbe robustly models the residual probe effects that MAT model cannot explain. When applied to analyzing ChIP-chip data, TileProbe performs consistently better than MAT across a variety of analytical conditions. This shows that TileProbe resolves the issue of probe-specific effects more completely.

Availability: http://www.biostat.jhsph.edu/~hji/cisgenome/index_files/tileprobe.htm

Contact: hji{at}jhsph.edu

Supplementary information: Supplementary data are available at Bioinformatics online.

Associate Editor: John Quackenbush

Received on April 15, 2009; revised on June 16, 2009; accepted on July 7, 2009

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