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Journal of Nucleic Acids
Volume 2010, Article ID 489736, 6 pages
http://dx.doi.org/10.4061/2010/489736
Research Article

A Comparative Study of the Impact of G-Stack Probes on Various Affymetrix GeneChips of Mammalia

Departments of Mathematical Sciences and Biological Sciences, University of Essex, Wivenhoe Park, Colchester, Essex CO4 3SQ, UK

Received 1 December 2009; Revised 11 February 2010; Accepted 22 April 2010

Academic Editor: Jean Louis Mergny

Copyright © 2010 Farhat Naureen Memon et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Abstract

We have previously discovered that probes containing runs of four or more contiguous guanines are not reliable for measuring gene expression in the Human HG_U133A Affymetrix GeneChip data. These probes are not correlated with other members of their probe set, but they are correlated with each other. We now extend our analysis to different GeneChip designs of mouse, rat, and human. We find that, in all these chip designs, the G-stack probes (probes with a run of exactly four consecutive guanines) are correlated highly with each other, indicating that such probes are not reliable measures of gene expression in mammalian studies. Furthermore, there is no specific position of G-stack where the correlation is highest in all the chips. We also find that the latest designs of rat and mouse chips have significantly fewer G-stack probes compared to their predecessors, whereas there has not been a similar reduction in G-stack density across the changes in human chips. Moreover, we find significant changes in RMA values (after removing G-stack probes) as the number of G-stack probes increases.