For example, the MicroArray Quality Control (MAQC) project data shows only 70-85% concordance of qualitative gene calls (presence or absence) across different test sites using the same platform (i.e., a commercial microarray and its recommended labeling method) [ 7] and correlation coefficients of fold-change values ranging from 0.53 to 0.92 between platforms [ 8].
Our study mined data from a microarray project to find a total of 883 genes that showed a significant difference in expression between the sexes before the completion of sexual differentiation.
A collaborative microarray project (based on Affymetrix ATH1 arrays), dubbed AtGenExpress, has utilized 79 different Arabidopsis samples in triplicate to generate expression data [29], [30].
Though the 1000 Genomes Project data allowed a comprehensive survey of the SNPs in this particular array, the same approach can certainly be applied to other microarray platforms.
Because both EST sequencing projects and microarray projects generate large amounts of data, we have adopted the Stanford Microarray Database (SMD) [20] [24] open source platform developed at the University of Texas, the Longhorn Array Database (LAD) [25] to integrate microarray data with EST sequences, clustered consensus sequences, and homology annotation data.
E.J.F.: Designed project, performed microarray, analyzed data, wrote and edited manuscript.
Data normalization was performed using R statistical software http://www.r-project.org; microarray data were normalized across all arrays using the cyclic loess approach [ 36].
The correlation signature projects heterogeneous microarray expression data onto a coherent information space where a gene is represented by the vector of its correlations against a series of landmark genes.
GenoScript (http://genoscript.pasteur.fr/, Moreira et al., 2002) is such a web application, it can handle microbial microarray experiment data from small projects or large consortium programs, with a private access to unpublished data.
CJ initiated the project; participated in experimental designs, microarray and data interpretation, and manuscript drafting; and critically revised the manuscript.
