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Motif effects in Affymetrix GeneChips seriously affect probe intensities
An Affymetrix GeneChip consists of an array of hundreds of thousands of probes (each a sequence of 25 bases) with the probe values being used to infer the extent to which genes are expressed in the biological material under investigation. In this article, we demonstrate that these probe values are a...
Autores principales: | , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2012
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3479185/ https://www.ncbi.nlm.nih.gov/pubmed/22904084 http://dx.doi.org/10.1093/nar/gks717 |
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author | Upton, Graham J. G. Harrison, Andrew P. |
author_facet | Upton, Graham J. G. Harrison, Andrew P. |
author_sort | Upton, Graham J. G. |
collection | PubMed |
description | An Affymetrix GeneChip consists of an array of hundreds of thousands of probes (each a sequence of 25 bases) with the probe values being used to infer the extent to which genes are expressed in the biological material under investigation. In this article, we demonstrate that these probe values are also strongly influenced by their precise base sequence. We use data from >28 000 CEL files relating to 10 different Affymetrix GeneChip platforms and involving nearly 1000 experiments. Our results confirm known effects (those due to the T7-primer and the formation of G-quadruplexes) but reveal other effects. We show that there can be huge variations from one experiment to another, and that there may also be sizeable disparities between batches within an experiment and between CEL files within a batch. |
format | Online Article Text |
id | pubmed-3479185 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2012 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-34791852012-10-24 Motif effects in Affymetrix GeneChips seriously affect probe intensities Upton, Graham J. G. Harrison, Andrew P. Nucleic Acids Res Molecular Biology An Affymetrix GeneChip consists of an array of hundreds of thousands of probes (each a sequence of 25 bases) with the probe values being used to infer the extent to which genes are expressed in the biological material under investigation. In this article, we demonstrate that these probe values are also strongly influenced by their precise base sequence. We use data from >28 000 CEL files relating to 10 different Affymetrix GeneChip platforms and involving nearly 1000 experiments. Our results confirm known effects (those due to the T7-primer and the formation of G-quadruplexes) but reveal other effects. We show that there can be huge variations from one experiment to another, and that there may also be sizeable disparities between batches within an experiment and between CEL files within a batch. Oxford University Press 2012-10 2012-08-13 /pmc/articles/PMC3479185/ /pubmed/22904084 http://dx.doi.org/10.1093/nar/gks717 Text en © The Author(s) 2012. Published by Oxford University Press. http://creativecommons.org/licenses/by-nc/3.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/3.0), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Molecular Biology Upton, Graham J. G. Harrison, Andrew P. Motif effects in Affymetrix GeneChips seriously affect probe intensities |
title | Motif effects in Affymetrix GeneChips seriously affect probe intensities |
title_full | Motif effects in Affymetrix GeneChips seriously affect probe intensities |
title_fullStr | Motif effects in Affymetrix GeneChips seriously affect probe intensities |
title_full_unstemmed | Motif effects in Affymetrix GeneChips seriously affect probe intensities |
title_short | Motif effects in Affymetrix GeneChips seriously affect probe intensities |
title_sort | motif effects in affymetrix genechips seriously affect probe intensities |
topic | Molecular Biology |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3479185/ https://www.ncbi.nlm.nih.gov/pubmed/22904084 http://dx.doi.org/10.1093/nar/gks717 |
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