ArticleJournal of nucleic acids2010
A Comparative Study of the Impact of G-Stack Probes on Various Affymetrix GeneChips of Mammalia.
Article in Journal of nucleic acids, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.
What it found
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Who cites it
5 citing papers in PubMed.
- Sequence characteristics define trade-offs between on-target and genome-wide off-target hybridization of oligoprobes.PloS one · 2018Article
- Optimization of signal-to-noise ratio for efficient microarray probe design.Bioinformatics (Oxford, England) · 2016Article
- Sources of high variance between probe signals in Affymetrix short oligonucleotide microarrays.Sensors (Basel, Switzerland) · 2013Article
- Motif effects in Affymetrix GeneChips seriously affect probe intensities.Nucleic acids research · 2012Article
- Normalized Affymetrix expression data are biased by G-quadruplex formation.Nucleic acids research · 2012Article
Corrections and comments
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Authors and funding
3 authors.
Funding
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 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.
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Registered trials
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