Analysis of matched mRNA measurements from two different microarray technologies

W. P. Kuo, T.-K. Jenssen, A. J. Butte, L. Ohno-Machado, I. S. Kohane
2002 Bioinformatics  
† These authors contributed equally to this work. Running head: Analysis of mRNA measurements from two microarray techs. Abstract Motivation: The existence of several technologies for measuring gene expression makes the question of cross-technology agreement of measurements an important issue. Crossplatform utilization of data from different technologies has the potential to reduce the need to duplicate experiments but requires corresponding measurements to be comparable. Methods: A comparison
more » ... f mRNA measurements of 2,895 sequence-matched genes in 56 cell lines from the standard panel of 60 cancer cell lines from the National Cancer Institute (NCI 60) was carried out by calculating correlation between matched measurements and calculating concordance between cluster from two high-throughput DNA microarray technologies, Stanford type cDNA microarrays and Affymetrix oligonucleotide microarrays. Results: In general, corresponding measurements from the two platforms showed poor correlation. Clusters of genes and cell lines were discordant between the two technologies, suggesting that relative intra-technology relationships were not preserved. GC-content, sequence length, average signal intensity, and an estimator of crosshybridization were found to be associated with the degree of correlation. This suggest gene-specific, or more correctly probe-specific, factors influencing measurements differently in the two platforms, implying a poor prognosis for a broad utilization of gene expression measurements across platforms.
doi:10.1093/bioinformatics/18.3.405 pmid:11934739 fatcat:rtngqqayz5hpxovvbv4qiaoffy