Bioinformatics Vol. 19 no. 8 2003
Pages 956-965
© 2003 Oxford University Press
Microarray standard data set and figures of merit for comparing data processing methods and experiment designs
Rosetta Inpharmatics Inc.,
,12 040
115th Avenue Northeast, Kirkland, WA 98034, USA
Received on July 24, 2002
; revised on October 16, 2002 and December 17, 2002
; accepted on December 22, 2002
Motivation: There is a very large and growing level of effort toward improving the platforms, experiment designs, and data analysis methods for microarray expression profiling. Along with a growing richness in the approaches there is a growing confusion among most scientists as to how to make objective comparisons and choices between them for different applications. There is a need for a standard framework for the microarray community to compare and improve analytical and statistical methods.
Results: We report on a microarray data set comprising 204
in-situ synthesized oligonucleotide arrays, each
hybridized with two-color cDNA samples derived from 20
different human tissues and cell lines. Design of the 
24 000
60mer oligonucleotides that report 2500 known
genes on the arrays, and design of the hybridization
experiments, were carried out in a way that supports the
performance assessment of alternative data processing
approaches and of alternative experiment and array designs. We
also propose standard figures of merit for success in detecting
individual differential expression changes or expression levels,
and for detecting similarities and differences in expression
patterns across genes and experiments. We expect this data set
and the proposed figures of merit will provide a standard
framework for much of the microarray community to compare and
improve many analytical and statistical methods relevant to
microarray data analysis, including image processing,
normalization, error modeling, combining of multiple reporters
per gene, use of replicate experiments, and sample referencing
schemes in measurements based on expression change.
Availability/Supplementary information: Expression data and supplementary information are available at http://www.rii.com/publications/2003/HE_SDS.htm
Contact: yudong_he{at}merck.com
* To whom correspondence should be addressed.
A wholly owned subsidiary of Merck & Co., Inc.
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