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The IronChip evaluation package: a package of perl modules for robust analysis of custom microarrays

Yevhen Vainshtein123*, Mayka Sanchez124, Alvis Brazma5, Matthias W Hentze12, Thomas Dandekar3* and Martina U Muckenthaler12*

Author Affiliations

1 MMPU, Department of Pediatric Oncology, Hematology and Immunology, University of Heidelberg D-69120 Heidelberg, Germany

2 European Molecular Biology Laboratory, D-69117 Heidelberg, Germany

3 Department of Bioinformatics, University of Wurzburg, Biozentrum, Am Hubland, D-97074 Wurzburg, Germany

4 IMPPC, Institute of Predictive and Personalized Medicine of Cancer, Crta Can Ruti, Cami de les Escoles s/n 08916 Badalona, Barcelona, Spain

5 European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK

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BMC Bioinformatics 2010, 11:112  doi:10.1186/1471-2105-11-112

Published: 1 March 2010



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.


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.


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: webcite