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CrossHybDetector: detection of cross-hybridization events in DNA microarray experiments
BACKGROUND: DNA microarrays contain thousands of different probe sequences represented on their surface. These are designed in such a way that potential cross-hybridization reactions with non-target sequences are minimized. However, given the large number of probes, the occurrence of cross hybridiza...
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Formato: | Texto |
Lenguaje: | English |
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BioMed Central
2008
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Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2596149/ https://www.ncbi.nlm.nih.gov/pubmed/19014642 http://dx.doi.org/10.1186/1471-2105-9-485 |
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author | Uva, Paolo de Rinaldis, Emanuele |
author_facet | Uva, Paolo de Rinaldis, Emanuele |
author_sort | Uva, Paolo |
collection | PubMed |
description | BACKGROUND: DNA microarrays contain thousands of different probe sequences represented on their surface. These are designed in such a way that potential cross-hybridization reactions with non-target sequences are minimized. However, given the large number of probes, the occurrence of cross hybridization events cannot be excluded. This problem can dramatically affect the data quality and cause false positive/false negative results. RESULTS: CrossHybDetector is a software package aimed at the identification of cross-hybridization events occurred during individual array hybridization, by using the probe sequences and the array intensity values. As output, the software provides the user with a list of array spots potentially 'corrupted' and their associated p-values calculated by Monte Carlo simulations. Graphical plots are also generated, which provide a visual and global overview of the quality of the microarray experiment with respect to cross-hybridization issues. CONCLUSION: CrossHybDetector is implemented as a package for the statistical computing environment R and is freely available under the LGPL license within the CRAN project. |
format | Text |
id | pubmed-2596149 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2008 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-25961492008-12-05 CrossHybDetector: detection of cross-hybridization events in DNA microarray experiments Uva, Paolo de Rinaldis, Emanuele BMC Bioinformatics Software BACKGROUND: DNA microarrays contain thousands of different probe sequences represented on their surface. These are designed in such a way that potential cross-hybridization reactions with non-target sequences are minimized. However, given the large number of probes, the occurrence of cross hybridization events cannot be excluded. This problem can dramatically affect the data quality and cause false positive/false negative results. RESULTS: CrossHybDetector is a software package aimed at the identification of cross-hybridization events occurred during individual array hybridization, by using the probe sequences and the array intensity values. As output, the software provides the user with a list of array spots potentially 'corrupted' and their associated p-values calculated by Monte Carlo simulations. Graphical plots are also generated, which provide a visual and global overview of the quality of the microarray experiment with respect to cross-hybridization issues. CONCLUSION: CrossHybDetector is implemented as a package for the statistical computing environment R and is freely available under the LGPL license within the CRAN project. BioMed Central 2008-11-17 /pmc/articles/PMC2596149/ /pubmed/19014642 http://dx.doi.org/10.1186/1471-2105-9-485 Text en Copyright © 2008 Uva and de Rinaldis; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( (http://creativecommons.org/licenses/by/2.0) ), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Software Uva, Paolo de Rinaldis, Emanuele CrossHybDetector: detection of cross-hybridization events in DNA microarray experiments |
title | CrossHybDetector: detection of cross-hybridization events in DNA microarray experiments |
title_full | CrossHybDetector: detection of cross-hybridization events in DNA microarray experiments |
title_fullStr | CrossHybDetector: detection of cross-hybridization events in DNA microarray experiments |
title_full_unstemmed | CrossHybDetector: detection of cross-hybridization events in DNA microarray experiments |
title_short | CrossHybDetector: detection of cross-hybridization events in DNA microarray experiments |
title_sort | crosshybdetector: detection of cross-hybridization events in dna microarray experiments |
topic | Software |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2596149/ https://www.ncbi.nlm.nih.gov/pubmed/19014642 http://dx.doi.org/10.1186/1471-2105-9-485 |
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