title: Matching of array CGH and gene expression microarray features for the purpose of integrative genomic analyses.
abstract: BACKGROUND
  An increasing number of genomic studies interrogating more than one molecular level is published. Bioinformatics follows biological practice, and recent years have seen a surge in methodology for the integrative analysis of genomic data. Often such analyses require knowledge of which elements of one platform link to those of another. Although important, many integrative analyses do not or insufficiently detail the matching of the platforms.
  
  
  RESULTS
  We describe, illustrate and discuss six matching procedures. They are implemented in the R-package sigaR (available from Bioconductor). The principles underlying the presented matching procedures are generic, and can be combined to form new matching approaches or be applied to the matching of other platforms. Illustration of the matching procedures on a variety of data sets reveals how the procedures differ in the use of the available data, and may even lead to different results for individual genes.
  
  
  CONCLUSIONS
  Matching of data from multiple genomics platforms is an important preprocessing step for many integrative bioinformatic analysis, for which we present six generic procedures, both old and new. They have been implemented in the R-package sigaR, available from Bioconductor.
authors.affiliation: Department of Epidemiology and Biostatistics, VU University Medical Center, Amsterdam, The Netherlands. w.vanwieringen@vumc.nl
authors.forename: Wessel N
authors.initials: WN
authors.lastname: van Wieringen
authors.forename: Kristian
authors.initials: K
authors.lastname: Unger
authors.forename: Gwenaël G R
authors.initials: GG
authors.lastname: Leday
authors.forename: Oscar
authors.initials: O
authors.lastname: Krijgsman
authors.forename: Renée X
authors.initials: RX
authors.lastname: de Menezes
authors.forename: Bauke
authors.initials: B
authors.lastname: Ylstra
authors.forename: Mark A
authors.initials: MA
authors.lastname: van de Wiel
mesh_terms: D055028:Comparative Genomic Hybridization; D056915:DNA Copy Number Variations; D015870:Gene Expression; D020869:Gene Expression Profiling; D023281:Genomics / Q000379:methods; D020411:Oligonucleotide Array Sequence Analysis; D012984:Software