BGX: a Bioconductor package for the Bayesian integrated analysis of Affymetrix GeneChips.

ABSTRACT:

Background

Affymetrix 3' GeneChip microarrays are widely used to profile the expression of thousands of genes simultaneously. They differ from many other microarray types in that GeneChips are hybridised using a single labelled extract and because they contain multiple 'match' and 'mismatch' sequences for each transcript. Most algorithms extract the signal from GeneChip experiments in a sequence of separate steps, including background correction and normalisation, which inhibits the simultaneous use of all available information. They principally provide a point estimate of gene expression and, in contrast to BGX, do not fully integrate the uncertainty arising from potentially heterogeneous responses of the probes.

Results

BGX is a new Bioconductor R package that implements a

SUBMITTER: Turro E 

PROVIDER: S-EPMC2216047 | biostudies-literature | 2007 Nov

REPOSITORIES: biostudies-literature