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Thawing Frozen Robust Multi-array Analysis (fRMA)

BACKGROUND: A novel method of microarray preprocessing - Frozen Robust Multi-array Analysis (fRMA) - has recently been developed. This algorithm allows the user to preprocess arrays individually while retaining the advantages of multi-array preprocessing methods. The frozen parameter estimates requi...

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Detalles Bibliográficos
Autores principales: McCall, Matthew N, Irizarry, Rafael A
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2011
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3180392/
https://www.ncbi.nlm.nih.gov/pubmed/21923903
http://dx.doi.org/10.1186/1471-2105-12-369
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author McCall, Matthew N
Irizarry, Rafael A
author_facet McCall, Matthew N
Irizarry, Rafael A
author_sort McCall, Matthew N
collection PubMed
description BACKGROUND: A novel method of microarray preprocessing - Frozen Robust Multi-array Analysis (fRMA) - has recently been developed. This algorithm allows the user to preprocess arrays individually while retaining the advantages of multi-array preprocessing methods. The frozen parameter estimates required by this algorithm are generated using a large database of publicly available arrays. Curation of such a database and creation of the frozen parameter estimates is time-consuming; therefore, fRMA has only been implemented on the most widely used Affymetrix platforms. RESULTS: We present an R package, frmaTools, that allows the user to quickly create his or her own frozen parameter vectors. We describe how this package fits into a preprocessing workflow and explore the size of the training dataset needed to generate reliable frozen parameter estimates. This is followed by a discussion of specific situations in which one might wish to create one's own fRMA implementation. For a few specific scenarios, we demonstrate that fRMA performs well even when a large database of arrays in unavailable. CONCLUSIONS: By allowing the user to easily create his or her own fRMA implementation, the frmaTools package greatly increases the applicability of the fRMA algorithm. The frmaTools package is freely available as part of the Bioconductor project.
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spelling pubmed-31803922011-09-27 Thawing Frozen Robust Multi-array Analysis (fRMA) McCall, Matthew N Irizarry, Rafael A BMC Bioinformatics Software BACKGROUND: A novel method of microarray preprocessing - Frozen Robust Multi-array Analysis (fRMA) - has recently been developed. This algorithm allows the user to preprocess arrays individually while retaining the advantages of multi-array preprocessing methods. The frozen parameter estimates required by this algorithm are generated using a large database of publicly available arrays. Curation of such a database and creation of the frozen parameter estimates is time-consuming; therefore, fRMA has only been implemented on the most widely used Affymetrix platforms. RESULTS: We present an R package, frmaTools, that allows the user to quickly create his or her own frozen parameter vectors. We describe how this package fits into a preprocessing workflow and explore the size of the training dataset needed to generate reliable frozen parameter estimates. This is followed by a discussion of specific situations in which one might wish to create one's own fRMA implementation. For a few specific scenarios, we demonstrate that fRMA performs well even when a large database of arrays in unavailable. CONCLUSIONS: By allowing the user to easily create his or her own fRMA implementation, the frmaTools package greatly increases the applicability of the fRMA algorithm. The frmaTools package is freely available as part of the Bioconductor project. BioMed Central 2011-09-16 /pmc/articles/PMC3180392/ /pubmed/21923903 http://dx.doi.org/10.1186/1471-2105-12-369 Text en Copyright © 2011 McCall and Irizarry; licensee BioMed Central Ltd. https://creativecommons.org/licenses/by/2.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0 (https://creativecommons.org/licenses/by/2.0/) ), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Software
McCall, Matthew N
Irizarry, Rafael A
Thawing Frozen Robust Multi-array Analysis (fRMA)
title Thawing Frozen Robust Multi-array Analysis (fRMA)
title_full Thawing Frozen Robust Multi-array Analysis (fRMA)
title_fullStr Thawing Frozen Robust Multi-array Analysis (fRMA)
title_full_unstemmed Thawing Frozen Robust Multi-array Analysis (fRMA)
title_short Thawing Frozen Robust Multi-array Analysis (fRMA)
title_sort thawing frozen robust multi-array analysis (frma)
topic Software
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3180392/
https://www.ncbi.nlm.nih.gov/pubmed/21923903
http://dx.doi.org/10.1186/1471-2105-12-369
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