Probabilistic Analysis of Probe Reliability in Differential Gene Expression Studies with Short Oligonucleotide Arrays

Authors:
Leo Lahti;Laura L. Elo;Tero Aittokallio;Samuel Kaski
Affiliations:
Helsinki University of Technology, TKK;University of Turku, Turku;University of Turku, Turku;Helsinki University of Technology, TKK
Venue:
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Year:
2011

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Abstract

Probe defects are a major source of noise in gene expression studies. While existing approaches detect noisy probes based on external information such as genomic alignments, we introduce and validate a targeted probabilistic method for analyzing probe reliability directly from expression data and independently of the noise source. This provides insights into the various sources of probe-level noise and gives tools to guide probe design.