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

Memon, Farhat Naureen and Upton, Graham JG and Harrison, Andrew P (2010) 'A Comparative Study of the Impact of G-Stack Probes on Various Affymetrix GeneChips of Mammalia.' Journal of Nucleic Acids, 2010. pp. 1-6. ISSN 2090-0201


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<jats:p>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<mml:math xmlns:mml=""><mml:msup><mml:mn>3</mml:mn><mml:mo>′</mml:mo></mml:msup></mml:math>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.</jats:p>

Item Type: Article
Subjects: Q Science > QH Natural history > QH301 Biology
Q Science > QH Natural history > QH426 Genetics
Divisions: Faculty of Science and Health
Faculty of Science and Health > Mathematical Sciences, Department of
SWORD Depositor: Elements
Depositing User: Elements
Date Deposited: 07 Sep 2011 13:46
Last Modified: 15 Jan 2022 00:45

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