affyGG: computational protocols for genetical genomics with Affymetrix arrays.
BACKGROUND
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.


BACKGROUND
http://gbic.biol.rug.nl/supplementary.
Alberts
Rudi
R
Groningen Bioinformatics Centre, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Haren, The Netherlands.
Vera
Gonzalo
G
Jansen
Ritsert C
RC
D000465:Algorithms; D000818:Animals; D002874:Chromosome Mapping / Q000379:methods*; D004252:DNA Mutational Analysis / Q000379:methods*; D015342:DNA Probes / Q000235:genetics*; D006801:Humans; D051379:Mice; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D040641:Quantitative Trait Loci / Q000235:genetics*; D012984:Software
D015342:DNA Probes