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Open Access Research article

Probe-level linear model fitting and mixture modeling results in high accuracy detection of differential gene expression

Sébastien Lemieux

Author Affiliations

Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, Canada

BMC Bioinformatics 2006, 7:391  doi:10.1186/1471-2105-7-391

Published: 25 August 2006

Abstract

Background

The identification of differentially expressed genes (DEGs) from Affymetrix GeneChips arrays is currently done by first computing expression levels from the low-level probe intensities, then deriving significance by comparing these expression levels between conditions. The proposed PL-LM (Probe-Level Linear Model) method implements a linear model applied on the probe-level data to directly estimate the treatment effect. A finite mixture of Gaussian components is then used to identify DEGs using the coefficients estimated by the linear model. This approach can readily be applied to experimental design with or without replication.

Results

On a wholly defined dataset, the PL-LM method was able to identify 75% of the differentially expressed genes within 10% of false positives. This accuracy was achieved both using the three replicates per conditions available in the dataset and using only one replicate per condition.

Conclusion

The method achieves, on this dataset, a higher accuracy than the best set of tools identified by the authors of the dataset, and does so using only one replicate per condition.