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Bioinformatics Advance Access published online on December 16, 2007
Bioinformatics, doi:10.1093/bioinformatics/btm614
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© The Author (2007). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

affyGG: Computational protocols for genetical genomics with Affymetrix arrays

Rudi Alberts a, Gonzalo Vera a and Ritsert C. Jansen a,*

aGroningen Bioinformatics Centre, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Haren, the Netherlands

*To whom correspondence should be addressed. Ritsert C. Jansen, E-mail: r.c.jansen{at}rug.nl


  Abstract

Motivation: Affymetrix arrays use multiple probes per gene to measure mRNA abundances. Standard software takes averages over probes. Important information may be lost if polymorphisms in the mRNA affect the hybridization of individual probes.

Results: We present custom software to analyze genetical genomics experiments in human, mouse and other organisms: (i) an R package providing functions for QTL analysis at the individual probe level, and (ii) Perl scripts providing custom tracks in the UCSC Genome Browser to check for sequence polymorphisms in probe regions.

Availability: http://gbic.biol.rug.nl/supplementary.

Contact: r.c.jansen{at}rug.nl

Associate Editor: Prof. John Quackenbush

Received on July 4, 2007; revised on November 22, 2007; accepted on December 10, 2007

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