ArticleBioinformatics (Oxford, England)2009
TileProbe: modeling tiling array probe effects using publicly available data.
Article in Bioinformatics (Oxford, England), 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
8 citing papers in PubMed.
- High-resolution characterization of CPD hotspot formation in human fibroblasts.Nucleic acids research · 2014Article
- ChIPXpress: using publicly available gene expression data to improve ChIP-seq and ChIP-chip target gene ranking.BMC bioinformatics · 2013Article
- Group normalization for genomic data.PloS one · 2012Article
- hmChIP: a database and web server for exploring publicly available human and mouse ChIP-seq and ChIP-chip data.Bioinformatics (Oxford, England) · 2011Article
- Article
- MM-ChIP enables integrative analysis of cross-platform and between-laboratory ChIP-chip or ChIP-seq data.Genome biology · 2011Article
- JAMIE: joint analysis of multiple ChIP-chip experiments.Bioinformatics (Oxford, England) · 2010Article
- Starr: Simple Tiling ARRay analysis of Affymetrix ChIP-chip data.BMC bioinformatics · 2010Article
Corrections and comments
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Authors and funding
2 authors.
Funding
Abstract
motivationIndividual 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.
resultsWe 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/ approximately hji/cisgenome/index_files/tileprobe.htm.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.