InSiIicoDb: an R/Bioconductor package for accessing human Affymetrix expert-curated datasets from GEO

Jonatan Taminau, David Steenhoff, Alain Coletta, Stijn Meganck, Vasile Cosmin Lazar, Virginie De Schaetzen Van Brienen, Robin Duqué, Colin Molter, Hugues Bersini, Ann Nowe, David Y. Weiss-Solis

Research output: Contribution to journalArticle

Abstract

Microarray technology has become an integral part of biomedical research and increasing amounts of datasets become available through public repositories. However, re-use of these datasets is severely hindered by unstructured, missing, or incorrect biological samples information; as well as the wide variety of preprocessing methods in use. The inSilicoDb RBioconductor package is a command-line front-end to the InSilico DB, a web- based database currently containing 86,104 expert-curated human Affymetrix expression profiles compiled from 1,937 GEO repository series. The use of this package builds on the Bioconductor project's focus on reproducibility by enabling a clear workflow in which not only analysis, but also the retrieval of verified data, is supported.
Original languageEnglish
Pages (from-to)3204-3205
Number of pages2
JournalBioinformatics
Volume22
Issue number27
Publication statusPublished - 2011

Keywords

  • microarray data

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