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Motif effects in Affymetrix GeneChips seriously affect probe intensities

Upton, GJG and Harrison, AP (2012) 'Motif effects in Affymetrix GeneChips seriously affect probe intensities.' Nucleic Acids Research, 40 (19). 9705 - 9716. ISSN 0305-1048

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Abstract

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. © 2012 The Author(s).

Item Type: Article
Subjects: Q Science > Q Science (General)
Divisions: Faculty of Science and Health > Mathematical Sciences, Department of
Depositing User: Andrew Harrison
Date Deposited: 02 Feb 2013 18:07
Last Modified: 23 Jan 2019 00:18
URI: http://repository.essex.ac.uk/id/eprint/5414

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