Consistency analysis of redundant probe sets on affymetrix three-prime expression arrays and applications to differential mRNA processing.

ABSTRACT: Affymetrix three-prime expression microarrays contain thousands of redundant probe sets that interrogate different regions of the same gene. Differential expression analysis methods rarely consider probe redundancy, which can lead to inaccurate inference about overall gene expression or cause investigators to overlook potentially valuable information about differential regulation of variant mRNA products. We investigated the behaviour and consistency of redundant probe sets in a publicly-available data set containing samples from mouse brain amygdala and hippocampus and asked how applying filtering methods to the data affected consistency of results obtained from redundant probe sets. A genome-based filter that screens and groups probe sets according to their overlapping genomic alignments

SUBMITTER: Cui X 

PROVIDER: S-EPMC2621337 | biostudies-literature | 2009

REPOSITORIES: biostudies-literature