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Nucleic Acids Research 2006 34(9):e70; doi:10.1093/nar/gkl122
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Published online 24 May 2006

© The Author 2006. Published by Oxford University Press. All rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions@oxfordjournals.org

Methods Online

Relationship between gene expression and observed intensities in DNA microarrays—a modeling study

G. A. Held*, G. Grinstein and Y. Tu

IBM TJ Watson Research Center PO Box 218, Yorktown Heights, NY 10598, USA

*To whom correspondence should be addressed. Tel: +1 914 945 2609; Fax: +1 914 945 2141; Email: gaheld{at}us.ibm.com

Received October 28, 2005. Revised December 28, 2005. Accepted March 13, 2006.

A theoretical study of the physical properties which determine the variation in signal strength from probe to probe on a microarray is presented. A model which incorporates probe-target hybridization, as well as the subsequent dissociation which occurs during stringent washing of the microarray, is introduced and shown to reasonably describe publicly available spike-in experiments carried out at Affymetrix. In particular, this model suggests that probe-target dissociation during the stringent wash plays a critical role in determining the observed hybridization intensities. In addition, it is demonstrated that non-specific hybridization introduces uncertainties which significantly limit the ability of any model to accurately quantify absolute gene expression levels while, in contrast, target folding appears to have little effect on these results. Finally, for data from target spike-in experiments, our model is shown to compare favorably with an existing statistical model in determining target concentration levels.


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