A re-annotation pipeline for Illumina BeadArrays: improving the interpretation of gene expression data
Nuno L Barbosa-Morais, Mark J Dunning, Shamith A Samarajiwa, Jeremy FJ Darot, Matthew E Ritchie, Andy G Lynch, Simon Tavare
NUCLEIC ACIDS RESEARCH | OXFORD UNIV PRESS | Published : 2010
Illumina BeadArrays are among the most popular and reliable platforms for gene expression profiling. However, little external scrutiny has been given to the design, selection and annotation of BeadArray probes, which is a fundamental issue in data quality and interpretation. Here we present a pipeline for the complete genomic and transcriptomic re-annotation of Illumina probe sequences, also applicable to other platforms, with its output available through a Web interface and incorporated into Bioconductor packages. We have identified several problems with the design of individual probes and we show the benefits of probe re-annotation on the analysis of BeadArray gene expression data sets. We..View full abstract
Awarded by Cancer Research UK
Cancer Research UK (to N.L.B.M., M.J.D., S. A. S., A. G. L. and S. T.); Medical Research Council (to M.J.D.); European Molecular Biology Organization (to J.F.J.D); Isaac Newton Trust (to M. E. R.). Funding for open access charge: Cancer Research UK.