Methodology article

Determining gene expression on a single pair of microarrays

Robert W Reid and Anthony A Fodor

Department of Bioinformatics and Genomics, The University of North Carolina at Charlotte, 9201 University City Boulevard, Charlotte, NC 28223, USA

author email corresponding author email

BMC Bioinformatics 2008, 9:489doi:10.1186/1471-2105-9-489

Published:	21 November 2008

Abstract

Background

In microarray experiments the numbers of replicates are often limited due to factors such as cost, availability of sample or poor hybridization. There are currently few choices for the analysis of a pair of microarrays where N = 1 in each condition. In this paper, we demonstrate the effectiveness of a new algorithm called PINC (PINC is Not Cyber-T) that can analyze Affymetrix microarray experiments.

Results

PINC treats each pair of probes within a probeset as an independent measure of gene expression using the Bayesian framework of the Cyber-T algorithm and then assigns a corrected p-value for each gene comparison.

The p-values generated by PINC accurately control False Discovery rate on Affymetrix control data sets, but are small enough that family-wise error rates (such as the Holm's step down method) can be used as a conservative alternative to false discovery rate with little loss of sensitivity on control data sets.

Conclusion

PINC outperforms previously published methods for determining differentially expressed genes when comparing Affymetrix microarrays with N = 1 in each condition. When applied to biological samples, PINC can be used to assess the degree of variability observed among biological replicates in addition to analyzing isolated pairs of microarrays.