title: GeneRegionScan: a Bioconductor package for probe-level analysis of specific, small regions of the genome.
abstract: CONCLUSIONS
  Whole-genome microarrays allow us to interrogate the entire transcriptome of a cell. Affymetrix microarrays are constructed using several probes that match to different regions of a gene and a summarization step reduces this complexity into a single value, representing the expression level of the gene or the expression level of an exon in the case of exon arrays. However, this simplification eliminates information that might be useful when focusing on specific genes of interest. To address these limitations, we present a software package for the R platform that allows detailed analysis of expression at the probe level. The package matches the probe sequences against a target gene sequence (either mRNA or DNA) and shows the expression levels of each probe along the gene. It also features functions to fit a linear regression based on several genetic models that enables study of the relationship between gene expression and genotype.
  
  
  METHODS
  The software is implemented as a platform-independent R package available through the Bioconductor repository at http://www.bioconductor.org/. It is licensed as GPL 2.0.
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Center for Molecular Medicine, Karolinska Institute, Stockholm, Sweden. lasse.folkersen@ki.se
authors.forename: Lasse
authors.initials: L
authors.lastname: Folkersen
authors.forename: Diego
authors.initials: D
authors.lastname: Diez
authors.forename: Craig E
authors.initials: CE
authors.lastname: Wheelock
authors.forename: Jesper Z
authors.initials: JZ
authors.lastname: Haeggström
authors.forename: Susumu
authors.initials: S
authors.lastname: Goto
authors.forename: Per
authors.initials: P
authors.lastname: Eriksson
authors.forename: Anders
authors.initials: A
authors.lastname: Gabrielsen
mesh_terms: D003198:Computer Simulation; D030541:Databases, Genetic; D016678:Genome; D005838:Genotype; D008957:Models, Genetic; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D016415:Sequence Alignment; D012984:Software; D014584:User-Computer Interface