title: The IronChip evaluation package: a package of perl modules for robust analysis of custom microarrays.
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/
authors.affiliation: MMPU, Department of Pediatric Oncology, Hematology and Immunology, University of Heidelberg, Heidelberg, Germany. vainshte@embl.de
authors.forename: Yevhen
authors.initials: Y
authors.lastname: Vainshtein
authors.forename: Mayka
authors.initials: M
authors.lastname: Sanchez
authors.forename: Alvis
authors.initials: A
authors.lastname: Brazma
authors.forename: Matthias W
authors.initials: MW
authors.lastname: Hentze
authors.forename: Thomas
authors.initials: T
authors.lastname: Dandekar
authors.forename: Martina U
authors.initials: MU
authors.lastname: Muckenthaler
mesh_terms: D000465:Algorithms; D030541:Databases, Genetic; D020869:Gene Expression Profiling / Q000379:methods; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D011381:Programming Languages; D012984:Software