FRMA ST: Frozen robust multiarray analysis for Affymetrix Exon and Gene ST arrays

Matthew N. McCall; Harris A. Jaffee; Rafael A. Irizarry

doi:10.1093/bioinformatics/bts588

FRMA ST: Frozen robust multiarray analysis for Affymetrix Exon and Gene ST arrays

Matthew N. McCall, Harris A. Jaffee, Rafael A. Irizarry

Research output: Contribution to journal › Article › peer-review

27 Scopus citations

Abstract

Frozen robust multiarray analysis (fRMA) is a single-array preprocessing algorithm that retains the advantages of multiarray algorithms and removes certain batch effects by downweighting probes that have high between-batch residual variance. Here, we extend the fRMA algorithm to two new microarray platforms-Affymetrix Human Exon and Gene 1.0 ST-by modifying the fRMA probe-level model and extending the frma package to work with oligo ExonFeatureSet and GeneFeatureSet objects.

Original language	English (US)
Pages (from-to)	3153-3154
Number of pages	2
Journal	Bioinformatics
Volume	28
Issue number	23
DOIs	https://doi.org/10.1093/bioinformatics/bts588
State	Published - Dec 2012
Externally published	Yes

ASJC Scopus subject areas

Statistics and Probability
Biochemistry
Molecular Biology
Computer Science Applications
Computational Theory and Mathematics
Computational Mathematics

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10.1093/bioinformatics/bts588

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title = "FRMA ST: Frozen robust multiarray analysis for Affymetrix Exon and Gene ST arrays",

abstract = "Frozen robust multiarray analysis (fRMA) is a single-array preprocessing algorithm that retains the advantages of multiarray algorithms and removes certain batch effects by downweighting probes that have high between-batch residual variance. Here, we extend the fRMA algorithm to two new microarray platforms-Affymetrix Human Exon and Gene 1.0 ST-by modifying the fRMA probe-level model and extending the frma package to work with oligo ExonFeatureSet and GeneFeatureSet objects.",

author = "McCall, {Matthew N.} and Jaffee, {Harris A.} and Irizarry, {Rafael A.}",

note = "Funding Information: Funding: This work was funded by National Institutes of Health (CA009363 to M.N.M.), National Institutes of Health (GM083084, RR021967 and GM103552 to H.A.J.) and partially funded by National Institutes of Health (GM083084, RR021967 and UL1RR025005 to R.A.I.).",

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doi = "10.1093/bioinformatics/bts588",

language = "English (US)",

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AU - McCall, Matthew N.

AU - Jaffee, Harris A.

AU - Irizarry, Rafael A.

N1 - Funding Information: Funding: This work was funded by National Institutes of Health (CA009363 to M.N.M.), National Institutes of Health (GM083084, RR021967 and GM103552 to H.A.J.) and partially funded by National Institutes of Health (GM083084, RR021967 and UL1RR025005 to R.A.I.).

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FRMA ST: Frozen robust multiarray analysis for Affymetrix Exon and Gene ST arrays

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