On probe-level interference and noise modeling in gene expression microarray experiments

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Abstract

This paper describes a signal processing model of gene expression microarray experiments using oligonucleotide technologies. The objective is to estimate the expression transcript concentrations modeled as an analog signal vector. This vector is received via a cascade of two noisy channels that model noise (uncertainty) before, during, and after hybridization. The second channel is also mixing since transcript-probe hybridization is not perfectly specific. The gene expression levels are estimated based on a second-order statistical model that incorporates biological, sample preparation, hybridization, and optical detection noises. A key feature is the explicit modeling of gene-specific and non-specific hybridization in which both have deterministic and random components. The model is applied to the processing of probe pairs as used in Affymetrix arrays, and comparison of currently used methods with the optimum Gauss-Markov estimator. In general, the estimation performance is a function of the hybridization noise characteristics, probe set design and number of experimental replicates, with implications for integrated design of the experimental process.

Original languageEnglish (US)
Title of host publicationEuropean Signal Processing Conference
StatePublished - 2006
Externally publishedYes
Event14th European Signal Processing Conference, EUSIPCO 2006 - Florence, Italy
Duration: Sep 4 2006Sep 8 2006

Other

Other14th European Signal Processing Conference, EUSIPCO 2006
CountryItaly
CityFlorence
Period9/4/069/8/06

Fingerprint

Microarrays
Gene expression
Oligonucleotides
Experiments
Signal processing
Genes
Processing

ASJC Scopus subject areas

  • Signal Processing
  • Electrical and Electronic Engineering

Cite this

On probe-level interference and noise modeling in gene expression microarray experiments. / Flikkema, Paul G.

European Signal Processing Conference. 2006.

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Flikkema, PG 2006, On probe-level interference and noise modeling in gene expression microarray experiments. in European Signal Processing Conference. 14th European Signal Processing Conference, EUSIPCO 2006, Florence, Italy, 9/4/06.
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