Analysis of matched mRNA measurements from two different microarray technologies.
BACKGROUND
[corrected] The existence of several technologies for measuring gene expression makes the question of cross-technology agreement of measurements an important issue. Cross-platform 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 of mRNA measurements of 2895 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 cross-hybridization were found to be associated with the degree of correlation. This suggests 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.
Kuo
Winston Patrick
WP
Children's Hospital Informatics Program and Division of Endocrinology, Department of Medicine, Children's Hospital, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA. wpkuo@mit.edu
Jenssen
Tor-Kristian
TK
Butte
Atul J
AJ
Ohno-Machado
Lucila
L
Kohane
Isaac S
IS
D016000:Cluster Analysis; D030561:Databases, Nucleic Acid; D015870:Gene Expression / Q000235:genetics; D015972:Gene Expression Regulation, Neoplastic / Q000235:genetics*; D006801:Humans; D009317:National Library of Medicine (U.S.); D020411:Oligonucleotide Array Sequence Analysis / Q000295:instrumentation / Q000379:methods* / Q000592:standards; D012333:RNA, Messenger / Q000032:analysis*; D015203:Reproducibility of Results; D012680:Sensitivity and Specificity; D014407:Tumor Cells, Cultured; D014481:United States
D012333:RNA, Messenger