title: User-friendly solutions for microarray quality control and pre-processing on ArrayAnalysis.org.
abstract: Quality control (QC) is crucial for any scientific method producing data. Applying adequate QC introduces new challenges in the genomics field where large amounts of data are produced with complex technologies. For DNA microarrays, specific algorithms for QC and pre-processing including normalization have been developed by the scientific community, especially for expression chips of the Affymetrix platform. Many of these have been implemented in the statistical scripting language R and are available from the Bioconductor repository. However, application is hampered by lack of integrative tools that can be used by users of any experience level. To fill this gap, we developed a freely available tool for QC and pre-processing of Affymetrix gene expression results, extending, integrating and harmonizing functionality of Bioconductor packages. The tool can be easily accessed through a wizard-like web portal at http://www.arrayanalysis.org or downloaded for local use in R. The portal provides extensive documentation, including user guides, interpretation help with real output illustrations and detailed technical documentation. It assists newcomers to the field in performing state-of-the-art QC and pre-processing while offering data analysts an integral open-source package. Providing the scientific community with this easily accessible tool will allow improving data quality and reuse and adoption of standards.
authors.affiliation: Department of Bioinformatics-BiGCaT, Maastricht University, PO Box 616, 6200 MD Maastricht, The Netherlands. l.eijssen@maastrichtuniversity.nl
authors.forename: Lars M T
authors.initials: LM
authors.lastname: Eijssen
authors.forename: Magali
authors.initials: M
authors.lastname: Jaillard
authors.forename: Michiel E
authors.initials: ME
authors.lastname: Adriaens
authors.forename: Stan
authors.initials: S
authors.lastname: Gaj
authors.forename: Philip J
authors.initials: PJ
authors.lastname: de Groot
authors.forename: Michael
authors.initials: M
authors.lastname: Müller
authors.forename: Chris T
authors.initials: CT
authors.lastname: Evelo
mesh_terms: D020869:Gene Expression Profiling / Q000379:methods / Q000592:standards*; D020407:Internet; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods / Q000592:standards*; D011786:Quality Control; D012984:Software; D014584:User-Computer Interface