Research article

A study of inter-lab and inter-platform agreement of DNA microarray data

Huixia Wang¹ , Xuming He¹ , Mark Band² , Carole Wilson² and Lei Liu²

¹  Department of Statistics, University of Illinois at Urbana-Champaign, 101 Illini Hall, 725 South Wright Street, Champaign, Illinois 61820, USA

²  W. M. Keck Center for Comparative and Functional Genomics, University of Illinois at Urbana-Champaign, 1201 W. Gregory Drive, Urbana, Illinois 61801, USA

author email corresponding author email

BMC Genomics 2005, 6:71doi:10.1186/1471-2164-6-71

Published:	11 May 2005

Abstract

As gene expression profile data from DNA microarrays accumulate rapidly, there is a natural need to compare data across labs and platforms. Comparisons of microarray data can be quite challenging due to data complexity and variability. Different labs may adopt different technology platforms. One may ask about the degree of agreement we can expect from different labs and different platforms. To address this question, we conducted a study of inter-lab and inter-platform agreement of microarray data across three platforms and three labs. The statistical measures of consistency and agreement used in this paper are the Pearson correlation, intraclass correlation, kappa coefficients, and a measure of intra-transcript correlation. The three platforms used in the present paper were Affymetrix GeneChip, custom cDNA arrays, and custom oligo arrays. Using the within-platform variability as a benchmark, we found that these technology platforms exhibited an acceptable level of agreement, but the agreement between two technologies within the same lab was greater than that between two labs using the same technology. The consistency of replicates in each experiment varies from lab to lab. When there is high consistency among replicates, different technologies show good agreement within and across labs using the same RNA samples. On the other hand, the lab effect, especially when confounded with the RNA sample effect, plays a bigger role than the platform effect on data agreement.