The IronChip evaluation package: a package of perl modules for robust analysis of custom microarrays
Author
Vainshtein, Yevhen
Sanchez, Mayka
Brazma, Alvis
W. Hentze, Matthias
Dandekar, Thomas
Muckenthaler, Martina U.
Publication date
2010ISSN
1471-2105
Abstract
Background: Gene expression studies greatly contribute to our understanding of complex relationships in gene regulatory networks. However, the complexity of array design, production and manipulations are limiting factors, affecting data quality. The use of customized DNA microarrays improves overall data quality in many situations, however, only if for these specifically designed microarrays analysis tools are available. Results: The IronChip Evaluation Package (ICEP) is a collection of Perl utilities and an easy to use data evaluation pipeline for the analysis of microarray data with a focus on data quality of custom-designed microarrays. The package has been developed for the statistical and bioinformatical analysis of the custom cDNA microarray IronChip but can be easily adapted for other cDNA or oligonucleotide-based designed microarray platforms. ICEP uses decision tree-based algorithms to assign quality flags and performs robust analysis based on chip design properties regarding multiple repetitions, ratio cut-off, background and negative controls. Conclusions: ICEP is a stand-alone Windows application to obtain optimal data quality from custom-designed microarrays and is freely available here (see "Additional Files" section) and at: http://www.alice-dsl.net/evgeniy.vainshtein/ICEP/
Document Type
Article
Document version
Published version
Language
English
Subject (CDU)
57 - Biological sciences in general
Keywords
Estudis d'expressió gènica
ADN
Genoma
Microarrays d'ADN
Estudios de expresión génica
ADN
Genoma
Microarrays de ADN
Gene expression studies
DNA
Genome
DNA microarrays
Pages
7
Publisher
Springer Nature
Collection
11;
Is part of
BMC Bioinformatics
Citation
Vainshtein, Yevhen; Sanchez, Mayka; Brazma, Alvis [et al.]. The IronChip evaluation package: a package of perl modules for robust analysis of custom microarrays. BMC Bioinformatics, 2010, 11, 112. Disponible en: <https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-11-112>. Fecha de acceso: 18 ene. 2022. DOI: 10.1186/1471-2105-11-112
This item appears in the following Collection(s)
- Ciències de la Salut [736]
Rights
This article is published under license to BioMed Central Ltd. 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.
Except where otherwise noted, this item's license is described as http://creativecommons.org/licenses/by/2.0