BeadArray Expression Analysis Using Bioconductor
- Author(s)
- Ritchie, ME; Dunning, MJ; Smith, ML; Shi, W; Lynch, AG;
- Details
- Publication Year 2011-12,Volume 7,Issue #12,Page e1002276.
- Journal Title
- PLOS COMPUTATIONAL BIOLOGY
- Publication Type
- Journal Article
- Abstract
- Illumina whole-genome expression BeadArrays are a popular choice in gene profiling studies. Aside from the vendor-provided software tools for analyzing BeadArray expression data (GenomeStudio/BeadStudio), there exists a comprehensive set of open-source analysis tools in the Bioconductor project, many of which have been tailored to exploit the unique properties of this platform. In this article, we explore a number of these software packages and demonstrate how to perform a complete analysis of BeadArray data in various formats. The key steps of importing data, performing quality assessments, preprocessing, and annotation in the common setting of assessing differential expression in designed experiments will be covered.
- Publisher
- PUBLIC LIBRARY SCIENCE
- Keywords
- GENE-EXPRESSION; MICROARRAY DATA; BACKGROUND CORRECTION; ILLUMINA MICROARRAY; IDENTIFICATION; VALIDATION; AFFYMETRIX; PLATFORMS; PROFILES; PROBES
- Research Division(s)
- Bioinformatics
- Publisher's Version
- https://doi.org/10.1371/journal.pcbi.1002276
- Open Access at Publisher's Site
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3228778/- Terms of Use/Rights Notice
- Copyright Ritchie et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Creation Date: 2011-12-01 12:00:00