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Bioinformatics. 2012 Dec 1;28(23):3153-4. doi: 10.1093/bioinformatics/bts588. Epub 2012 Oct 7.

fRMA ST: frozen robust multiarray analysis for Affymetrix Exon and Gene ST arrays.

Author information

1
Department of Biostatistics and Computational Biology, University of Rochester Medical Center, 265 Crittenden Blvd., CU 420630, Rochester, NY 14642, USA. mccallm@gmail.com

Abstract

SUMMARY:

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.

AVAILABILITY AND IMPLEMENTATION:

All packages are implemented in R. Source code and binaries are freely available through the Bioconductor project. Convenient links to all software and data packages can be found at http://mnmccall.com/software

CONTACT:

mccallm@gmail.com.

PMID:
23044545
PMCID:
PMC3509489
DOI:
10.1093/bioinformatics/bts588
[Indexed for MEDLINE]
Free PMC Article

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