Rudi Alberts1, Gonzalo Vera, Ritsert C Jansen. 1. Groningen Bioinformatics Centre, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Haren, The Netherlands.
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.
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.
Authors: Daniel C Ciobanu; Lu Lu; Khyobeni Mozhui; Xusheng Wang; Manjunatha Jagalur; John A Morris; William L Taylor; Klaus Dietz; Perikles Simon; Robert W Williams Journal: Genetics Date: 2009-11-02 Impact factor: 4.562
Authors: Morris A Swertz; K Joeri van der Velde; Bruno M Tesson; Richard A Scheltema; Danny Arends; Gonzalo Vera; Rudi Alberts; Martijn Dijkstra; Paul Schofield; Klaus Schughart; John M Hancock; Damian Smedley; Katy Wolstencroft; Carole Goble; Engbert O de Brock; Andrew R Jones; Helen E Parkinson; Ritsert C Jansen Journal: Genome Biol Date: 2010-03-09 Impact factor: 13.583