A framework for oligonucleotide microarray preprocessing

Benilton S. Carvalho, Rafael A. Irizarry

Research output: Contribution to journalArticlepeer-review

Abstract

Motivation: The availability of flexible open source software for the analysis of gene expression raw level data has greatly facilitated the development of widely used preprocessing methods for these technologies. However, the expansion of microarray applications has exposed the limitation of existing tools. Results: We developed the oligo package to provide a more general solution that supports a wide range of applications. The package is based on the BioConductor principles of transparency, reproducibility and efficiency of development. It extends the existing tools and leverages existing code for visualization, accessing data and widely used preprocessing routines. The oligo package implements a unified paradigm for preprocessing data and interfaces with other BioConductor tools for downstream analysis. Our infrastructure is general and can be used by other BioConductor packages.

Original languageEnglish (US)
Article numberbtq431
Pages (from-to)2363-2367
Number of pages5
JournalBioinformatics
Volume26
Issue number19
DOIs
StatePublished - Aug 5 2010

ASJC Scopus subject areas

  • Statistics and Probability
  • Biochemistry
  • Molecular Biology
  • Computer Science Applications
  • Computational Theory and Mathematics
  • Computational Mathematics

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