TileProbe: Modeling tiling array probe effects using publicly available data

Jennifer Toolan Judy, Hongkai Ji

Research output: Contribution to journalArticlepeer-review

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 MATalgorithm 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.

Original languageEnglish (US)
Pages (from-to)2369-2375
Number of pages7
JournalBioinformatics
Volume25
Issue number18
DOIs
StatePublished - Sep 2009

ASJC Scopus subject areas

  • Statistics and Probability
  • Biochemistry
  • Molecular Biology
  • Computer Science Applications
  • Computational Theory and Mathematics
  • Computational Mathematics

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