title: A user-friendly workflow for analysis of Illumina gene expression bead array data available at the arrayanalysis.org portal.
abstract: BACKGROUND
  Illumina whole-genome expression bead arrays are a widely used platform for transcriptomics. Most of the tools available for the analysis of the resulting data are not easily applicable by less experienced users. ArrayAnalysis.org provides researchers with an easy-to-use and comprehensive interface to the functionality of R and Bioconductor packages for microarray data analysis. As a modular open source project, it allows developers to contribute modules that provide support for additional types of data or extend workflows.
  
  
  RESULTS
  To enable data analysis of Illumina bead arrays for a broad user community, we have developed a module for ArrayAnalysis.org that provides a free and user-friendly web interface for quality control and pre-processing for these arrays. This module can be used together with existing modules for statistical and pathway analysis to provide a full workflow for Illumina gene expression data analysis. The module accepts data exported from Illumina's GenomeStudio, and provides the user with quality control plots and normalized data. The outputs are directly linked to the existing statistics module of ArrayAnalysis.org, but can also be downloaded for further downstream analysis in third-party tools.
  
  
  CONCLUSIONS
  The Illumina bead arrays analysis module is available at http://www.arrayanalysis.org . A user guide, a tutorial demonstrating the analysis of an example dataset, and R scripts are available. The module can be used as a starting point for statistical evaluation and pathway analysis provided on the website or to generate processed input data for a broad range of applications in life sciences research.
authors.affiliation: Department of Bioinformatics-BiGCaT, Maastricht University, Universiteitssingel 50, 6229 ER, Maastricht, The Netherlands. l.eijssen@maastrichtuniversity.nl.
authors.forename: Lars M T
authors.initials: LM
authors.lastname: Eijssen
authors.affiliation: TNO, Research Group Microbiology & Systems Biology, Utrechtseweg 48, 3704 HE, Zeist, The Netherlands. varshna.goelela@crl.com.|Current address: Charles River Laboratories, BioFocus, Discovery Services, Darwinweg 24, 2333 CR, Leiden, The Netherlands. varshna.goelela@crl.com.
authors.forename: Varshna S
authors.initials: VS
authors.lastname: Goelela
authors.affiliation: TNO, Research Group Microbiology & Systems Biology, Utrechtseweg 48, 3704 HE, Zeist, The Netherlands. thomas@edgeleap.com.|EdgeLeap B.V., Hooghiemstraplein 15, 3514 AX, Utrecht, The Netherlands. thomas@edgeleap.com.
authors.forename: Thomas
authors.initials: T
authors.lastname: Kelder
authors.affiliation: Department of Bioinformatics-BiGCaT, Maastricht University, Universiteitssingel 50, 6229 ER, Maastricht, The Netherlands. m.e.adriaens@amc.uva.nl.|Department of Experimental Cardiology, Academic Medical Center, Meibergdreef 9, 1100 DD, Amsterdam, The Netherlands. m.e.adriaens@amc.uva.nl.
authors.forename: Michiel E
authors.initials: ME
authors.lastname: Adriaens
authors.affiliation: Department of Bioinformatics-BiGCaT, Maastricht University, Universiteitssingel 50, 6229 ER, Maastricht, The Netherlands. chris.evelo@maastrichtuniversity.nl.
authors.forename: Chris T
authors.initials: CT
authors.lastname: Evelo
authors.affiliation: TNO, Research Group Microbiology & Systems Biology, Utrechtseweg 48, 3704 HE, Zeist, The Netherlands. marijana@edgeleap.com.|EdgeLeap B.V., Hooghiemstraplein 15, 3514 AX, Utrecht, The Netherlands. marijana@edgeleap.com.
authors.forename: Marijana
authors.initials: M
authors.lastname: Radonjic
mesh_terms: D019295:Computational Biology / Q000592:standards; D020407:Internet; D020411:Oligonucleotide Array Sequence Analysis; D011786:Quality Control; D014584:User-Computer Interface