Nucleic Acids Research, 2003, Vol. 31, No. 7 e36
© 2003 Oxford University Press
Data extraction from composite oligonucleotide microarrays
Cancer Genomics Laboratory, University of Texas M. D. Anderson Cancer Center, 1515 Holcombe Boulevard, Unit 85, Houston, TX 77030, USA and 1 Institute of Signal Processing, Tampere University of Technology, PO Box 553, 33101 Tampere, Finland
*To whom correspondence should be addressed. Tel: +1 713 745 1502; Fax: +1 713 792 5549; Email: is{at}ieee.org
Microarray or DNA chip technology is revolutionizing biology by empowering researchers in the collection of broad-scope gene information. It is well known that microarray-based measurements exhibit a substantial amount of variability due to a number of possible sources, ranging from hybridization conditions to image capture and analysis. In order to make reliable inferences and carry out quantitative analysis with microarray data, it is generally advisable to have more than one measurement of each gene. The availability of both between-array and within-array replicate measurements is essential for this purpose. Although statistical considerations call for increasing the number of replicates of both types, the latter is particularly challenging in practice due to a number of limiting factors, especially for in-house spotting facilities. We propose a novel approach to design so-called composite microarrays, which allow more replicates to be obtained without increasing the number of printed spots.