Thawing Frozen Robust Multi-array Analysis (fRMA)
<p>Abstract</p> <p>Background</p> <p>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 prep...
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doaj-1c2a7a38112a49deb539912961aaef4e2020-11-24T21:28:55ZengBMCBMC Bioinformatics1471-21052011-09-0112136910.1186/1471-2105-12-369Thawing Frozen Robust Multi-array Analysis (fRMA)Irizarry Rafael AMcCall Matthew N<p>Abstract</p> <p>Background</p> <p>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 <it>frozen </it>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.</p> <p>Results</p> <p>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.</p> <p>Conclusions</p> <p>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.</p> http://www.biomedcentral.com/1471-2105/12/369 |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Irizarry Rafael A McCall Matthew N |
spellingShingle |
Irizarry Rafael A McCall Matthew N Thawing Frozen Robust Multi-array Analysis (fRMA) BMC Bioinformatics |
author_facet |
Irizarry Rafael A McCall Matthew N |
author_sort |
Irizarry Rafael A |
title |
Thawing Frozen Robust Multi-array Analysis (fRMA) |
title_short |
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_sort |
thawing frozen robust multi-array analysis (frma) |
publisher |
BMC |
series |
BMC Bioinformatics |
issn |
1471-2105 |
publishDate |
2011-09-01 |
description |
<p>Abstract</p> <p>Background</p> <p>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 <it>frozen </it>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.</p> <p>Results</p> <p>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.</p> <p>Conclusions</p> <p>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.</p> |
url |
http://www.biomedcentral.com/1471-2105/12/369 |
work_keys_str_mv |
AT irizarryrafaela thawingfrozenrobustmultiarrayanalysisfrma AT mccallmatthewn thawingfrozenrobustmultiarrayanalysisfrma |
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