title: ArrayInitiative - a tool that simplifies creating custom Affymetrix CDFs.
abstract: BACKGROUND
  Probes on a microarray represent a frozen view of a genome and are quickly outdated when new sequencing studies extend our knowledge, resulting in significant measurement error when analyzing any microarray experiment. There are several bioinformatics approaches to improve probe assignments, but without in-house programming expertise, standardizing these custom array specifications as a usable file (e.g. as Affymetrix CDFs) is difficult, owing mostly to the complexity of the specification file format. However, without correctly standardized files there is a significant barrier for testing competing analysis approaches since this file is one of the required inputs for many commonly used algorithms. The need to test combinations of probe assignments and analysis algorithms led us to develop ArrayInitiative, a tool for creating and managing custom array specifications.
  
  
  RESULTS
  ArrayInitiative is a standalone, cross-platform, rich client desktop application for creating correctly formatted, custom versions of manufacturer-provided (default) array specifications, requiring only minimal knowledge of the array specification rules and file formats. Users can import default array specifications, import probe sequences for a default array specification, design and import a custom array specification, export any array specification to multiple output formats, export the probe sequences for any array specification and browse high-level information about the microarray, such as version and number of probes. The initial release of ArrayInitiative supports the Affymetrix 3' IVT expression arrays we currently analyze, but as an open source application, we hope that others will contribute modules for other platforms.
  
  
  CONCLUSIONS
  ArrayInitiative allows researchers to create new array specifications, in a standard format, based upon their own requirements. This makes it easier to test competing design and analysis strategies that depend on probe definitions. Since the custom array specifications are easily exported to the manufacturer's standard format, researchers can analyze these customized microarray experiments using established software tools, such as those available in Bioconductor.
authors.affiliation: Department of Bioinformatics and Genomics, University of North Carolina - Charlotte, Charlotte, NC 28223-0001, USA.
authors.forename: Christopher C
authors.initials: CC
authors.lastname: Overall
authors.forename: D Andrew
authors.initials: DA
authors.lastname: Carr
authors.forename: Ehsan S
authors.initials: ES
authors.lastname: Tabari
authors.forename: Kevin J
authors.initials: KJ
authors.lastname: Thompson
authors.forename: Jennifer W
authors.initials: JW
authors.lastname: Weller
mesh_terms: D000230:Adenocarcinoma / Q000235:genetics; D000465:Algorithms; D006801:Humans; D008175:Lung Neoplasms / Q000235:genetics; D046228:Microarray Analysis / Q000379:methods*; D015345:Oligonucleotide Probes; D012984:Software
chemical_list: D015345:Oligonucleotide Probes