An introduction to Pigeons

Pigeons is a standalone GUI program for the Windows platform under the .NET framework to analyze Affymetrix GeneChip data generated from cross-species experiments and was first released in late-April, 2010.

Pigeons allows the user to input and analyse microarray data for the XSpecies microarray approach. This can be DNA hybridisations across species, to determine empirical boundaries for custom Cell Description Files (CDF) files for XSpecies transcriptomics or to examine an experimental design to identify Single Feature Polymorphisms (SFP) either at the DNA or RNA level.

Pigeons provides an intuitive way to examine the signals at the individual oligonucleotides in a probe set and to compare them with the same probe sets from other hybridisations. Result can be exported as lists and as graphical representations for probe sets to assist in the interpretation of oligo-level data at the DNA or RNA level.

There are three main applications within this software package:

  • Pigeon Filter: is a cut-off analysis for the removal of poorly hybridising oligoprobes
  • Pigeon Mining & Image: provides fold-change analysis and statistical filters
  • Pigeon Query: is an interface for quick probe-set retrieval from datasets