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BMC Genomics  2005 

Three microarray platforms: an analysis of their concordance in profiling gene expression

DOI: 10.1186/1471-2164-6-63

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The three platforms had 6430 genes in common. In general, correlation of gene expression levels across the platforms was good when defined by concordance in the direction of expression difference (upregulation or downregulation), scatter plot analysis, principal component analysis, cell line correlation or quantitative RT-PCR. The overall correlations (r values) between platforms were in the range 0.7 to 0.8, as determined by analysis of scatter plots. When concordance was measured for expression ratios significant at p-values of <0.05 and at expression threshold levels of 1.5 and 2-fold, the agreement among the platforms was very high, ranging from 93% to 100%.Our results indicate that the long oligonucleotide platform is highly suitable for expression analysis and compares favorably with the cDNA and short oligonucleotide varieties. All three platforms can give similar and reproducible results if the criterion is the direction of change in gene expression and minimal emphasis is placed on the magnitude of change.Completion of the human genome sequence has made it possible to study expression of the entire complement of 20,000–30,000 genes in a single assay. The two most common array platforms are based on collections of cDNA clones [1] or short (25 base) oligonucleotides synthesized in situ by photolithographic methods (i.e., by Affymetrix, Inc.) [2]. Partly because they are easy to use, microarrays are the most extensively used technology for studying gene expression on a global scale [3,4]. Thousands of expression studies employ one or the other microarray platform, but comparison of results between platforms has been difficult because of inherent differences in the array technologies. The situation became more complex as investigators began using long oligonucleotide arrays for expression profiling [5-9].Because long oligonucleotide arrays for expression profiling are relatively new, we wished to validate them in relation to the cDNA and short oligonucleotide p


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