title: Reproducible probe-level analysis of the Affymetrix Exon 1.0 ST array with R/Bioconductor.
abstract: The presence of different transcripts of a gene across samples can be analysed by whole-transcriptome microarrays. Reproducing results from published microarray data represents a challenge owing to the vast amounts of data and the large variety of preprocessing and filtering steps used before the actual analysis is carried out. To guarantee a firm basis for methodological development where results with new methods are compared with previous results, it is crucial to ensure that all analyses are completely reproducible for other researchers. We here give a detailed workflow on how to perform reproducible analysis of the GeneChip®Human Exon 1.0 ST Array at probe and probeset level solely in R/Bioconductor, choosing packages based on their simplicity of use. To exemplify the use of the proposed workflow, we analyse differential splicing and differential gene expression in a publicly available dataset using various statistical methods. We believe this study will provide other researchers with an easy way of accessing gene expression data at different annotation levels and with the sufficient details needed for developing their own tools for reproducible analysis of the GeneChip®Human Exon 1.0 ST Array.
authors.forename: Maria
authors.initials: M
authors.lastname: Rodrigo-Domingo
authors.forename: Rasmus
authors.initials: R
authors.lastname: Waagepetersen
authors.forename: Julie Støve
authors.initials: JS
authors.lastname: Bødker
authors.forename: Steffen
authors.initials: S
authors.lastname: Falgreen
authors.forename: Malene Krag
authors.initials: MK
authors.lastname: Kjeldsen
authors.forename: Hans Erik
authors.initials: HE
authors.lastname: Johnsen
authors.forename: Karen
authors.initials: K
authors.lastname: Dybkær
authors.forename: Martin
authors.initials: M
authors.lastname: Bøgsted
mesh_terms: D017398:Alternative Splicing; D005091:Exons; D006801:Humans; D015203:Reproducibility of Results