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A Comparative Study of the Impact of G-Stack Probes on Various Affymetrix GeneChips of Mammalia
Joint Authors
Harrison, Andrew P.
Memon, Farhat Naureen
Upton, Graham J. G.
Source
Issue
Vol. 2010, Issue 2010 (31 Dec. 2010), pp.1-6, 6 p.
Publisher
Hindawi Publishing Corporation
Publication Date
2010-07-07
Country of Publication
Egypt
No. of Pages
6
Main Subjects
Abstract EN
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 3′ 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.
American Psychological Association (APA)
Memon, Farhat Naureen& Upton, Graham J. G.& Harrison, Andrew P.. 2010. A Comparative Study of the Impact of G-Stack Probes on Various Affymetrix GeneChips of Mammalia. Journal of Nucleic Acids،Vol. 2010, no. 2010, pp.1-6.
https://search.emarefa.net/detail/BIM-475702
Modern Language Association (MLA)
Memon, Farhat Naureen…[et al.]. A Comparative Study of the Impact of G-Stack Probes on Various Affymetrix GeneChips of Mammalia. Journal of Nucleic Acids No. 2010 (2010), pp.1-6.
https://search.emarefa.net/detail/BIM-475702
American Medical Association (AMA)
Memon, Farhat Naureen& Upton, Graham J. G.& Harrison, Andrew P.. A Comparative Study of the Impact of G-Stack Probes on Various Affymetrix GeneChips of Mammalia. Journal of Nucleic Acids. 2010. Vol. 2010, no. 2010, pp.1-6.
https://search.emarefa.net/detail/BIM-475702
Data Type
Journal Articles
Language
English
Notes
Includes bibliographical references
Record ID
BIM-475702