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Correcting positional correlations in Affymetrix® Genome Chips

We report and model a previously undescribed systematic error causing spurious excess correlations that depend on the distance between probes on Affymetrix® microarrays. The phenomenon affects pairs of features with large chip separations, up to over 100 probes apart. The effect may have a significa...

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Autores principales: Homouz, Dirar, Chen, Gang, Kudlicki, Andrzej S.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group 2015
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4649851/
https://www.ncbi.nlm.nih.gov/pubmed/25767049
http://dx.doi.org/10.1038/srep09078
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author Homouz, Dirar
Chen, Gang
Kudlicki, Andrzej S.
author_facet Homouz, Dirar
Chen, Gang
Kudlicki, Andrzej S.
author_sort Homouz, Dirar
collection PubMed
description We report and model a previously undescribed systematic error causing spurious excess correlations that depend on the distance between probes on Affymetrix® microarrays. The phenomenon affects pairs of features with large chip separations, up to over 100 probes apart. The effect may have a significant impact on analysis of correlations in large collections of expression data, where the systematic experimental errors are repeated in many data sets. Examples of such studies include analysis of functions and interactions in groups of genes, as well as global properties of genomes. We find that the average correlations between probes on Affymetrix microarrays are larger for smaller chip distances, which points out to a previously undescribed positional artifact. The magnitude of the artifact depends on the design of the chip, and we find it to be especially high for the yeast S98 microarray, where spurious excess correlations reach 0.1 at a distance of 50 probes. We have designed an algorithm to correct this bias and provide new data sets with the corrected expression values. This algorithm was successfully implemented to remove the positional artifact from the S98 chip data while preserving the integrity of the data.
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spelling pubmed-46498512015-11-23 Correcting positional correlations in Affymetrix® Genome Chips Homouz, Dirar Chen, Gang Kudlicki, Andrzej S. Sci Rep Article We report and model a previously undescribed systematic error causing spurious excess correlations that depend on the distance between probes on Affymetrix® microarrays. The phenomenon affects pairs of features with large chip separations, up to over 100 probes apart. The effect may have a significant impact on analysis of correlations in large collections of expression data, where the systematic experimental errors are repeated in many data sets. Examples of such studies include analysis of functions and interactions in groups of genes, as well as global properties of genomes. We find that the average correlations between probes on Affymetrix microarrays are larger for smaller chip distances, which points out to a previously undescribed positional artifact. The magnitude of the artifact depends on the design of the chip, and we find it to be especially high for the yeast S98 microarray, where spurious excess correlations reach 0.1 at a distance of 50 probes. We have designed an algorithm to correct this bias and provide new data sets with the corrected expression values. This algorithm was successfully implemented to remove the positional artifact from the S98 chip data while preserving the integrity of the data. Nature Publishing Group 2015-03-13 /pmc/articles/PMC4649851/ /pubmed/25767049 http://dx.doi.org/10.1038/srep09078 Text en Copyright © 2015, Macmillan Publishers Limited. All rights reserved http://creativecommons.org/licenses/by/4.0/ This work is licensed under a Creative Commons Attribution 4.0 International License. The images or other third party material in this article are included in the article's Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder in order to reproduce the material. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/
spellingShingle Article
Homouz, Dirar
Chen, Gang
Kudlicki, Andrzej S.
Correcting positional correlations in Affymetrix® Genome Chips
title Correcting positional correlations in Affymetrix® Genome Chips
title_full Correcting positional correlations in Affymetrix® Genome Chips
title_fullStr Correcting positional correlations in Affymetrix® Genome Chips
title_full_unstemmed Correcting positional correlations in Affymetrix® Genome Chips
title_short Correcting positional correlations in Affymetrix® Genome Chips
title_sort correcting positional correlations in affymetrix® genome chips
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4649851/
https://www.ncbi.nlm.nih.gov/pubmed/25767049
http://dx.doi.org/10.1038/srep09078
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