MMBGX: a method for estimating expression at the isoform level and detecting differential splicing using whole-transcript Affymetrix arrays.

ABSTRACT: Affymetrix has recently developed whole-transcript GeneChips-'Gene' and 'Exon' arrays-which interrogate exons along the length of each gene. Although each probe on these arrays is intended to hybridize perfectly to only one transcriptional target, many probes match multiple transcripts located in different parts of the genome or alternative isoforms of the same gene. Existing statistical methods for estimating expression do not take this into account and are thus prone to producing inflated estimates. We propose a method, Multi-Mapping Bayesian Gene eXpression (MMBGX), which disaggregates the signal at 'multi-match' probes. When applied to Gene arrays, MMBGX removes the upward bias of gene-level expression estimates. When applied to Exon arrays, it can further disaggregate the signal betwe

SUBMITTER: Turro E 

PROVIDER: S-EPMC2800219 | biostudies-literature | 2010 Jan

REPOSITORIES: biostudies-literature