CrossHybDetector: detection of cross-hybridization events in DNA microarray experiments
Paolo Uva1, Emanuele de Rinaldis
1Istituto di Ricerche di Biologia Molecolare, Merck Research Laboratories, Rome, Italy. paolo_uva@merck.com
BMC Bioinformatics
|November 19, 2008
Summary
CrossHybDetector identifies cross-hybridization in DNA microarrays, preventing false results. This software package helps ensure accurate data quality by flagging potentially corrupted array spots.
Area of Science:
- Genomics
- Bioinformatics
- Molecular Biology
Background:
- DNA microarrays utilize thousands of probe sequences to minimize cross-hybridization.
- Despite design efforts, cross-hybridization events can occur due to the high probe density.
- These events compromise data quality, leading to false positive and false negative outcomes.
Purpose of the Study:
- To develop a computational tool for identifying cross-hybridization in DNA microarray experiments.
- To provide researchers with a method for assessing and mitigating data inaccuracies caused by non-specific binding.
Main Methods:
- CrossHybDetector analyzes probe sequences and array intensity data.
- It employs Monte Carlo simulations to calculate p-values for potential cross-hybridization events.
- The software generates graphical plots for a visual overview of experimental quality.
Main Results:
- Identifies specific array spots potentially affected by cross-hybridization.
- Quantifies the likelihood of cross-hybridization using statistical measures (p-values).
- Provides visual diagnostics to assess the impact of cross-hybridization on microarray data.
Conclusions:
- CrossHybDetector is available as an R package within the CRAN project.
- The software is freely accessible under the LGPL license.
- It offers a valuable resource for improving the reliability of DNA microarray analyses.
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