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Microarrays 2014, 3(1), 1-23; doi:10.3390/microarrays3010001
Article

Pigeons: A Novel GUI Software for Analysing and Parsing High Density Heterologous Oligonucleotide Microarray Probe Level Data

1,2,†
,
1,3
 and
1,4,*
1 School of Biosciences, University of Nottingham, Sutton Bonington, Loughborough LE12 5RD, UK 2 Department of Informatics, King's College London, Strand, London WC2R 2LS, UK 3 Nottingham Arabidopsis Stock Centre (NASC), University of Nottingham, Sutton Bonington, Loughborough LE12 5RD, UK 4 Crops for the Future Research Centre, University of Nottingham Malaysia Campus (UNMC), Jalan Broga, Semenyih 43500, Malaysia The first author carried out the research at the University of Nottingham and is now at King's College London.
* Author to whom correspondence should be addressed.
Received: 11 November 2013 / Revised: 17 December 2013 / Accepted: 19 December 2013 / Published: 3 January 2014
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Abstract

Genomic DNA-based probe selection by using high density oligonucleotide arrays has recently been applied to heterologous species (Xspecies). With the advent of this new approach, researchers are able to study the genome and transcriptome of a non-model or an underutilised crop species through current state-of-the-art microarray platforms. However, a software package with a graphical user interface (GUI) to analyse and parse the oligonucleotide probe pair level data is still lacking when an experiment is designed on the basis of this cross species approach. A novel computer program called Pigeons has been developed for customised array data analysis to allow the user to import and analyse Affymetrix GeneChip® probe level data through XSpecies. One can determine empirical boundaries for removing poor probes based on genomic hybridisation of the test species to the Xspecies array, followed by making a species-specific Chip Description File (CDF) file for transcriptomics in the heterologous species, or Pigeons can be used to examine an experimental design to identify potential Single-Feature Polymorphisms (SFPs) at the DNA or RNA level. Pigeons is also focused around visualization and interactive analysis of the datasets. The software with its manual (the current release number version 1.2.1) is freely available at the website of the Nottingham Arabidopsis Stock Centre (NASC).
Keywords: affymetrix; heterologous microarray; oligonucleotide probe selection; Pigeons; probe pair data analysis; SFPs; Xspecies affymetrix; heterologous microarray; oligonucleotide probe selection; Pigeons; probe pair data analysis; SFPs; Xspecies
This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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Lai, H.-M.; May, S.T.; Mayes, S. Pigeons: A Novel GUI Software for Analysing and Parsing High Density Heterologous Oligonucleotide Microarray Probe Level Data. Microarrays 2014, 3, 1-23.

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